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Jin W, Deng Y, La Marca JE, Lelliott EJ, Diepstraten ST, König C, Tai L, Snetkova V, Dorighi KM, Hoberecht L, Hedditch MG, Whelan L, Healey G, Fayle D, Lau K, Potts MA, Chen MZ, Johnston APR, Liao Y, Shi W, Kueh AJ, Haley B, Fortin JP, Herold MJ. Advancing the genetic engineering toolbox by combining AsCas12a knock-in mice with ultra-compact screening. Nat Commun 2025; 16:974. [PMID: 39885149 PMCID: PMC11782673 DOI: 10.1038/s41467-025-56282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 01/09/2025] [Indexed: 02/01/2025] Open
Abstract
Cas12a is a next-generation gene editing tool that enables multiplexed gene targeting. Here, we present a mouse model that constitutively expresses enhanced Acidaminococcus sp. Cas12a (enAsCas12a) linked to an mCherry fluorescent reporter. We demonstrate efficient single and multiplexed gene editing in vitro, using primary and transformed cells from enAsCas12a mice. We further demonstrate successful in vivo gene editing, using normal and cancer-prone enAsCas12a stem cells to reconstitute the haematopoietic system of wild-type mice. We also present compact, genome-wide Cas12a knockout libraries, with four crRNAs per gene encoded across one (Scherzo) or two (Menuetto) vectors, and demonstrate the utility of these libraries across methodologies: in vitro enrichment and drop-out screening in lymphoma cells and immortalised fibroblasts, respectively, and in vivo screens to identify lymphoma-driving events. Finally, we demonstrate CRISPR multiplexing via simultaneous gene knockout (via Cas12a) and activation (via dCas9-SAM) using primary T cells and fibroblasts. Our enAsCas12a mouse and accompanying crRNA libraries enhance genome engineering capabilities and complement current CRISPR technologies.
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Affiliation(s)
- Wei Jin
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Yexuan Deng
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - John E La Marca
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Emily J Lelliott
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Christina König
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Lin Tai
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Valentina Snetkova
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
| | - Kristel M Dorighi
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
| | - Luke Hoberecht
- Computational Sciences, Genentech, Inc., South San Francisco, California, USA
| | - Millicent G Hedditch
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Lauren Whelan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Geraldine Healey
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Dan Fayle
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Kieran Lau
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Margaret A Potts
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Moore Z Chen
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Australia
| | - Angus P R Johnston
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Andrew J Kueh
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
- Université de Montréal, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Rosemont, Canada
| | | | - Marco J Herold
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia.
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia.
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Yadav R, Mahajan S, Singh H, Mehra NK, Madan J, Doijad N, Singh PK, Guru SK. Emerging In Vitro and In Vivo Models: Hope for the Better Understanding of Cancer Progression and Treatment. Adv Biol (Weinh) 2024; 8:e2300487. [PMID: 38581078 DOI: 10.1002/adbi.202300487] [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: 09/12/2023] [Revised: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Various cancer models have been developed to aid the understanding of the underlying mechanisms of tumor development and evaluate the effectiveness of various anticancer drugs in preclinical studies. These models accurately reproduce the critical stages of tumor initiation and development to mimic the tumor microenvironment better. Using these models for target validation, tumor response evaluation, resistance modeling, and toxicity comprehension can significantly enhance the drug development process. Herein, various in vivo or animal models are presented, typically consisting of several mice and in vitro models ranging in complexity from transwell models to spheroids and CRISPR-Cas9 technologies. While in vitro models have been used for decades and dominate the early stages of drug development, they are still limited primary to simplistic tests based on testing on a single cell type cultivated in Petri dishes. Recent advancements in developing new cancer therapies necessitate the generation of complicated animal models that accurately mimic the tumor's complexity and microenvironment. Mice make effective tumor models as they are affordable, have a short reproductive cycle, exhibit rapid tumor growth, and are simple to manipulate genetically. Human cancer mouse models are crucial to understanding the neoplastic process and basic and clinical research improvements. The following review summarizes different in vitro and in vivo metastasis models, their advantages and disadvantages, and their ability to serve as a model for cancer research.
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Affiliation(s)
- Rachana Yadav
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Srushti Mahajan
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, 500037, India
| | - Hoshiyar Singh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Neelesh Kumar Mehra
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, 500037, India
| | - Jitender Madan
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, 500037, India
| | - Nandkumar Doijad
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Pankaj Kumar Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, 500037, India
| | - Santosh Kumar Guru
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
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3
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Goel A, Rastogi A, Jain M, Niveriya K. RNA-based Therapeutics: Past, Present and Future Prospects, Challenges in Cancer Treatment. Curr Pharm Biotechnol 2024; 25:2125-2137. [PMID: 38347795 DOI: 10.2174/0113892010291042240130171709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 09/10/2024]
Abstract
It is becoming more and harder in today's climate to disregard the impact of cancer on social health. Even though a significant amount of money is spent annually on cancer research, it still ranks as the second leading cause of death worldwide. Additionally, only about half of the patients suffering from complex forms of cancer survive a year after receiving traditional cancer therapies. A method for silencing genes is called RNA interference (RNAi). Such a method is very effective in focusing on genes linked to cancer. Most gene products implicated in cancer have recently been used as RNA interference (RNAi) therapeutic targets. According to the findings from this research, RNAi application is necessary for today's cancer treatment to target functioning carcinogenic molecules and tumor resistance to chemotherapy and radiation. Proapoptotic and antiproliferative activity has been reported from previous research studies on cell culture systems, animal models, and clinical trials through the knockdown of gene products from RNAi technology. Numerous novel RNAi-based medications are now in the clinical trial stages thanks to the discovery of the RNAi mechanism and advancements in the area. In the future, genomic-based personalized medicines can be developed through this RNAi therapy. Hopefully, cancer sufferers will find this sort of therapy to be one of the most effective ones. Various kinds of RNA-based treatments, such as aptamers, small interfering RNAs, microRNAs, antisense oligonucleotides, and messenger RNA, are covered in broad terms in this study. We also present an overview of the RNA-based therapies that have received regulatory approval in the past or are now undergoing clinical studies.
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Affiliation(s)
- Anjana Goel
- Department of Biotechnology, GLA University, Mathura, India
| | - Amisha Rastogi
- Department of Biotechnology, GLA University, Mathura, India
| | - Mansi Jain
- Department of Biotechnology, GLA University, Mathura, India
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Zhang Y, Zhang X, Zhang Y, Xu H, Wei Z, Wang X, Li Y, Guo J, Wu F, Fang X, Pang L, Deng B, Yu D. c-Myc inhibits LAPTM5 expression in B-cell lymphomas. Ann Hematol 2023; 102:3499-3513. [PMID: 37713124 DOI: 10.1007/s00277-023-05434-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
Myc is a pivotal protooncogenic transcription factor that contributes to the development of almost all Burkitt's lymphomas and about one-third of diffuse large B-cell lymphomas. How B-cells sustain their uncontrolled proliferation due to high Myc is not yet well defined. Here, we found that Myc trans-represses the expression of murine LAPTM5, a gene coding a lysosome-associated protein, by binding to two E-boxes in the LAPTM5 promoter. While the product of intact mRNA (CDS+3'UTR) of LAPTM5 failed to suppress the growth of B-lymphomas, either the protein coded by coding sequence (CDS) itself or the non-coding 3'-untranslated region (3'UTR) mRNA was able to inhibit the growth of B-lymphomas. Moreover, Myc trans-activated miR-17-3p, which promoted tumor growth. Strikingly, LAPTM5 3'UTR contains 11 miR-17-3p-binding sites through which the LAPTM5 protein synthesis was inhibited. The functional interplay between low LAPTM5 mRNA and high miR-17-3p due to high Myc in B-lymphomas leads to further dampening of tumor-suppressive LAPTM5 protein, which promotes tumor progression. Our results indicate that Myc inhibits LAPTM5 expression in B-lymphoma cells by transcriptional and post-transcriptional modifications.
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Affiliation(s)
- Yanqing Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xin Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
- Department of Pathology, Sir Run Run Shaw Hospital, Institute of Clinical Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Han Xu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Zichen Wei
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xin Wang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Yan Li
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Junrong Guo
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Fan Wu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xiao Fang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Lei Pang
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Bin Deng
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Duonan Yu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China.
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5
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Hong Y, Ren T, Wang X, Liu X, Fei Y, Meng S, Han X, Sun C, Shen H, Li L, Qiu L, Qian Z, Zhou S, Zhang H, Wang X. APR-246 triggers ferritinophagy and ferroptosis of diffuse large B-cell lymphoma cells with distinct TP53 mutations. Leukemia 2022; 36:2269-2280. [PMID: 35835991 DOI: 10.1038/s41375-022-01634-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022]
Abstract
TP53 mutations correlate with inferior survival in many cancers. APR-246 is a compound to shift mutant p53 and exhibits anti-cancer effects. Among its effects, APR-246 facilitates the binding of restored p53 mutants to target genes and their transcription. A set of 2464 DLBCL cases from multiple cohorts including our center, was integrated to identify the type and localization of TP53 mutations and clinical impacts. APR-246 was applied in TP53-mutated DLBCL cells and xenograft mouse models to explore the anti-tumor effect. TP53 mutations frequency was 16% and TP53 mutations correlated with poor overall survival (OS) and progression-free survival (PFS) in all cases, especially in germinal center B-cell-like (GCB) and unclassified (UNC) subtypes. Notably, TP53 single mutations in the DNA binding domain (DBD) led to poor OS and PFS. Specifically, mutations in exon 7 correlated with poorer OS, while mutations in exons 5 and 6 associated with inferior PFS. APR-246 induces p53-dependent ferritinophagy of DLBCL cells with TP53 missense mutation on exon 7 and ferroptosis of DLBCL cells harboring wild-type TP53 and other TP53 mutations. TP53 mutations on exons 5, 6 and 7 are predictors of progression and survival. Targeting mutant p53 by APR-246 is a promising therapeutic approach for DLBCL patients.
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Affiliation(s)
- Yuheng Hong
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Tianyuan Ren
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Xiaoxuan Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Xia Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Yue Fei
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Shen Meng
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Xu Han
- Department of Statistics, North Carolina State University, Raleigh, NC, 27695-7555, USA
| | - Cong Sun
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Hongru Shen
- Department of Epidemiology and Biostatistics, Tianjin Cancer Institute, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, CN, China
| | - Lanfang Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Lihua Qiu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Zhengzi Qian
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Shiyong Zhou
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China.
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, 300060, CN, China.
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Ebrahimi N, Parkhideh S, Samizade S, Esfahani AN, Samsami S, Yazdani E, Adelian S, Chaleshtori SR, Shah-Amiri K, Ahmadi A, Aref AR. Crosstalk between lncRNAs in the apoptotic pathway and therapeutic targets in cancer. Cytokine Growth Factor Rev 2022; 65:61-74. [PMID: 35597701 DOI: 10.1016/j.cytogfr.2022.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/03/2022]
Abstract
The assertion that a significant portion of the mammalian genome has not been translated and that non-coding RNA accounts for over half of polyadenylate RNA have received much attention. In recent years, increasing evidence proposes non-coding RNAs (ncRNAs) as new regulators of various cellular processes, including cancer progression and nerve damage. Apoptosis is a type of programmed cell death critical for homeostasis and tissue development. Cancer cells often have inhibited apoptotic pathways. It has recently been demonstrated that up/down-regulation of various lncRNAs in certain types of tumors shapes cancer cells' response to apoptotic stimuli. This review discusses the most recent studies on lncRNAs and apoptosis in healthy and cancer cells. In addition, the role of lncRNAs as novel targets for cancer therapy is reviewed here. Finally, since it has been shown that lncRNA expression is associated with specific types of cancer, the potential for using lncRNAs as biomarkers is also discussed.
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Affiliation(s)
- Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Iran
| | - Sahar Parkhideh
- Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Setare Samizade
- Department of Cellular and molecular, School of Biological Sciences, Islamic Azad University of Falavarjan, Iran
| | - Alireza Nasr Esfahani
- Department of Cellular and molecular, School of Biological Sciences, Islamic Azad University of Falavarjan, Iran
| | - Sahar Samsami
- Biotechnology department of Fasa University of medical science, Fasa, Iran
| | - Elnaz Yazdani
- Department of Biology, Faculty of Science, University Of Isfahan, Isfahan, Iran; Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Samaneh Adelian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Kamal Shah-Amiri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr 75169, Iran.
| | - Amir Reza Aref
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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7
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Klimovich B, Meyer L, Merle N, Neumann M, König AM, Ananikidis N, Keber CU, Elmshäuser S, Timofeev O, Stiewe T. Partial p53 reactivation is sufficient to induce cancer regression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:80. [PMID: 35232479 PMCID: PMC8889716 DOI: 10.1186/s13046-022-02269-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 01/21/2023]
Abstract
Background Impaired p53 function is one of the central molecular features of a tumor cell and even a partial reduction in p53 activity can increase the cancer risk in mice and men. From a therapeutic perspective it is noteworthy that tumor cells often become addicted to the absence of p53 providing a rationale for developing p53 reactivating compounds to treat cancer patients. Unfortunately, many of the compounds that are currently undergoing preclinical and clinical testing fail to fully reactivate mutant p53 proteins, raising the crucial question: how much p53 activity is needed to elicit a therapeutic effect? Methods We have genetically modelled partial p53 reactivation using knock-in mice with inducible expression of the p53 variant E177R. This variant has a reduced ability to bind and transactivate target genes and consequently causes moderate cancer susceptibility. We have generated different syngeneically transplanted and autochthonous mouse models of p53-deficient acute myeloid leukemia and B or T cell lymphoma. After cancer manifestation we have activated E177R expression and analyzed the in vivo therapy response by bioluminescence or magnetic resonance imaging. The molecular response was further characterized in vitro by assays for gene expression, proliferation, senescence, differentiation, apoptosis and clonogenic growth. Results We report the conceptually intriguing observation that the p53 variant E177R, which promotes de novo leukemia and lymphoma formation, inhibits proliferation and viability, induces immune cell infiltration and triggers cancer regression in vivo when introduced into p53-deficient leukemia and lymphomas. p53-deficient cancer cells proved to be so addicted to the absence of p53 that even the low-level activity of E177R is detrimental to cancer growth. Conclusions The observation that a partial loss-of-function p53 variant promotes tumorigenesis in one setting and induces regression in another, underlines the highly context-specific effects of individual p53 mutants. It further highlights the exquisite sensitivity of cancer cells to even small changes in p53 activity and reveals that changes in activity level are more important than the absolute level. As such, the study encourages ongoing research efforts into mutant p53 reactivating drugs by providing genetic proof-of-principle evidence that incomplete p53 reactivation may suffice to elicit a therapeutic response. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02269-6.
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Affiliation(s)
- Boris Klimovich
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Laura Meyer
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Nastasja Merle
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Michelle Neumann
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Alexander M König
- Clinic of Diagnostic and Interventional Radiology, Core Facility 7T-small animal MRI, Philipps-University, Marburg, Germany
| | - Nikolaos Ananikidis
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Corinna U Keber
- Institute for Pathology, University Hospital Marburg, Philipps-University, Marburg, Germany
| | - Sabrina Elmshäuser
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany
| | - Oleg Timofeev
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany. .,German Center for Lung Research (DZL), Philipps-University, Marburg, Germany.
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany. .,German Center for Lung Research (DZL), Philipps-University, Marburg, Germany. .,Genomics Core Facility, Philipps-University, Marburg, Germany.
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8
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Powell G, Pavlovic Djuranovic S, Djuranovic S. Gene dosage effects of poly(A) track-engineered hypomorphs. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:865-878. [PMID: 34729253 PMCID: PMC8536507 DOI: 10.1016/j.omtn.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Manipulation of gene activity through creation of hypomorphic mutants has been a long-standing tool in examining gene function. Our previous studies have indicated that hypomorphic mutants could be created by inserting cis-regulatory sequences composed of consecutive adenosine nucleotides called poly(A) tracks. Here we use poly(A) tracks to create hypomorphic mutants and functional characterization of membrane, secretory, and endogenous proteins. Insertion of poly(A) tracks into the sequences of interleukin-2 and membrane protein CD20 results in a programmable reduction of mRNA stability and attenuation of protein expression regardless of the presence of a signaling sequence. Likewise, CRISPR-Cas9 targeted insertion of poly(A) tracks into the coding sequence of the endogenous human genes AUF1 and TP53 results in a programmable reduction of targeted protein and mRNA levels. Functional analyses of AUF1-engineered hypomorphs indicate a direct correlation between AUF1 gene levels and the stability of AUF1-regulated mRNAs. Hypomorphs of TP53 affect expression of the target genes differentially depending on the severity of the hypomorphic mutation. Finally, decreases in TP53 protein affect the same cellular pathways in poly(A) track-engineered cells as in cancer cells, indicating these variants’ biological relevance. These results highlight this technology’s power to create predictable, stable hypomorphs in recombinant or endogenous genes in combination with CRISPR-Cas9 engineering tools.
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Affiliation(s)
- Geralle Powell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
- Correspondence: Sergej Djuranovic, Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA.
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9
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Dawes JC, Uren AG. Forward and Reverse Genetics of B Cell Malignancies: From Insertional Mutagenesis to CRISPR-Cas. Front Immunol 2021; 12:670280. [PMID: 34484175 PMCID: PMC8414522 DOI: 10.3389/fimmu.2021.670280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer genome sequencing has identified dozens of mutations with a putative role in lymphomagenesis and leukemogenesis. Validation of driver mutations responsible for B cell neoplasms is complicated by the volume of mutations worthy of investigation and by the complex ways that multiple mutations arising from different stages of B cell development can cooperate. Forward and reverse genetic strategies in mice can provide complementary validation of human driver genes and in some cases comparative genomics of these models with human tumors has directed the identification of new drivers in human malignancies. We review a collection of forward genetic screens performed using insertional mutagenesis, chemical mutagenesis and exome sequencing and discuss how the high coverage of subclonal mutations in insertional mutagenesis screens can identify cooperating mutations at rates not possible using human tumor genomes. We also compare a set of independently conducted screens from Pax5 mutant mice that converge upon a common set of mutations observed in human acute lymphoblastic leukemia (ALL). We also discuss reverse genetic models and screens that use CRISPR-Cas, ORFs and shRNAs to provide high throughput in vivo proof of oncogenic function, with an emphasis on models using adoptive transfer of ex vivo cultured cells. Finally, we summarize mouse models that offer temporal regulation of candidate genes in an in vivo setting to demonstrate the potential of their encoded proteins as therapeutic targets.
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Affiliation(s)
- Joanna C Dawes
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Anthony G Uren
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Pasqualucci L, Klein U. Mouse Models in the Study of Mature B-Cell Malignancies. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a034827. [PMID: 32398289 DOI: 10.1101/cshperspect.a034827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the past two decades, genomic analyses of several B-cell lymphoma entities have identified a large number of genes that are recurrently mutated, suggesting that their aberrant function promotes lymphomagenesis. For many of those genes, the specific role in normal B-cell development is unknown; moreover, whether and how their deregulated activity contributes to lymphoma initiation and/or maintenance is often difficult to determine. Genetically engineered mouse models that faithfully mimic lymphoma-associated genetic alterations represent valuable tools for elucidating the pathogenic roles of candidate oncogenes and tumor suppressors in vivo, as well as for the preclinical testing of novel therapeutic principles in an intact microenvironment. Here we summarize what has been learned about the mechanisms of oncogenic transformation from accurately modeling the most common and well-characterized genetic alterations identified in mature B-cell malignancies. This information is expected to guide the design of improved molecular diagnostics and mechanism-based therapeutic approaches for these diseases.
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Affiliation(s)
- Laura Pasqualucci
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, and the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | - Ulf Klein
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds LS9 7TF, United Kingdom
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11
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Sundara Rajan S, Ludwig KR, Hall KL, Jones TL, Caplen NJ. Cancer biology functional genomics: From small RNAs to big dreams. Mol Carcinog 2020; 59:1343-1361. [PMID: 33043516 PMCID: PMC7702050 DOI: 10.1002/mc.23260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katherine L. Hall
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
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12
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Albagli O, Maugein A, Huijbregts L, Bredel D, Carlier G, Martin P, Scharfmann R. New α- and SIN γ-retrovectors for safe transduction and specific transgene expression in pancreatic β cell lines. BMC Biotechnol 2019; 19:35. [PMID: 31208395 PMCID: PMC6580483 DOI: 10.1186/s12896-019-0531-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral vectors are invaluable tools to transfer genes and/or regulatory sequences into differentiated cells such as pancreatic cells. To date, several kinds of viral vectors have been used to transduce different pancreatic cell types, including insulin-producing β cells. However, few studies have used vectors derived from « simple » retroviruses, such as avian α- or mouse γ-retroviruses, despite their high experimental convenience. Moreover, such vectors were never designed to specifically target transgene expression into β cells. RESULTS We here describe two novel α- or SIN (Self-Inactivating) γ-retrovectors containing the RIP (Rat Insulin Promoter) as internal promoter. These two retrovectors are easily produced in standard BSL2 conditions, rapidly concentrated if needed, and harbor a large multiple cloning site. For the SIN γ-retrovector, either the VSV-G (pantropic) or the retroviral ecotropic (rodent specific) envelope was used. For the α-retrovector, we used the A type envelope, as its receptor, termed TVA, is only naturally present in avian cells and can efficiently be provided to mammalian β cells through either exogenous expression upon cDNA transfer or gesicle-mediated delivery of the protein. As expected, the transgenes cloned into the two RIP-containing retrovectors displayed a strong preferential expression in β over non-β cells compared to transgenes cloned in their non-RIP (CMV- or LTR-) regulated counterparts. We further show that RIP activity of both retrovectors mirrored fluctuations affecting endogenous INSULIN gene expression in human β cells. Finally, both α- and SIN γ-retrovectors were extremely poorly mobilized by the BXV1 xenotropic retrovirus, a common invader of human cells grown in immunodeficient mice, and, most notably, of human β cell lines. CONCLUSION Our novel α- and SIN γ-retrovectors are safe and convenient tools to stably and specifically express transgene(s) in mammalian β cells. Moreover, they both reproduce some regulatory patterns affecting INSULIN gene expression. Thus, they provide a helpful tool to both study the genetic control of β cell function and monitor changes in their differentiation status.
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Affiliation(s)
- Olivier Albagli
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France.
| | - Alicia Maugein
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France
| | - Lukas Huijbregts
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France
| | - Delphine Bredel
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France.,Present Address: Laboratoire de Recherche Translationnelle en Immunothérapie, Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France
| | - Géraldine Carlier
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France
| | - Patrick Martin
- Université Côte d'Azur, CNRS UMR7277 INSERM U1099, iBV (Institut de Biologie Valrose), Université Nice Sophia Antipolis, Bâtiment Sciences Naturelles; UFR Sciences, Parc Valrose, 28, avenue Valrose, 06108, Nice Cedex 2, France
| | - Raphaël Scharfmann
- INSERM U1016, CNRS UMR8104, Institut Cochin, Université Paris Descartes, 123 Boulevard de Port-Royal, 75014, Paris, France
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13
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Lin T, Hou PF, Meng S, Chen F, Jiang T, Li ML, Shi ML, Liu JJ, Zheng JN, Bai J. Emerging Roles of p53 Related lncRNAs in Cancer Progression: A Systematic Review. Int J Biol Sci 2019; 15:1287-1298. [PMID: 31223287 PMCID: PMC6567798 DOI: 10.7150/ijbs.33218] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
p53 is the major mediator of the tumor suppressor response. It participates in apoptosis and senescence and can respond to DNA damage. As a crucial sequence-specific transcription factor, p53 regulates the expression of many genes, such as small noncoding RNAs (ncRNAs), microRNAs, and long ncRNAs (lncRNAs). Given the emergence of novel and high-throughput sequencing technologies, many lncRNAs have been discovered. LncRNAs may function as vital gene regulators in a variety of biological processes through extensive mechanisms. Recently, lncRNAs have been demonstrated to be associated with the p53 regulatory pathway. In this review, we discuss the current and fast growing knowledge about the influence of lncRNAs to the p53 signaling pathway, the different mechanisms by which they affect gene expression in cancer. Our findings show that p53-associated lncRNAs may be used as biomarkers for cancer diagnosis or targets for disease therapy.
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Affiliation(s)
- Tian Lin
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Ping-Fu Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Sen Meng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Fang Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Tao Jiang
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Min-Le Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Mei-Lin Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jin-Jin Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
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14
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Shin YJ, Sa JK, Lee Y, Kim D, Chang N, Cho HJ, Son M, Oh MYT, Shin K, Lee JK, Park J, Jo YK, Kim M, Paddison PJ, Tergaonkar V, Lee J, Nam DH. PIP4K2A as a negative regulator of PI3K in PTEN -deficient glioblastoma. J Exp Med 2019; 216:1120-1134. [PMID: 30898893 PMCID: PMC6504209 DOI: 10.1084/jem.20172170] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 08/20/2018] [Accepted: 02/27/2019] [Indexed: 01/01/2023] Open
Abstract
Glioblastoma (GBM) is the most malignant brain tumor with profound genomic alterations. Tumor suppressor genes regulate multiple signaling networks that restrict cellular proliferation and present barriers to malignant transformation. While bona fide tumor suppressors such as PTEN and TP53 often undergo inactivation due to mutations, there are several genes for which genomic deletion is the primary route for tumor progression. To functionally identify putative tumor suppressors in GBM, we employed in vivo RNAi screening using patient-derived xenograft models. Here, we identified PIP4K2A, whose functional role and clinical relevance remain unexplored in GBM. We discovered that PIP4K2A negatively regulates phosphoinositide 3-kinase (PI3K) signaling via p85/p110 component degradation in PTEN-deficient GBMs and specifically targets p85 for proteasome-mediated degradation. Overexpression of PIP4K2A suppressed cellular and clonogenic growth in vitro and impeded tumor growth in vivo. Our results unravel a novel tumor-suppressive role of PIP4K2A for the first time and support the feasibility of combining oncogenomics with in vivo RNAi screen.
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Affiliation(s)
- Yong Jae Shin
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Yeri Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Donggeon Kim
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | | | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Miseol Son
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Division of Cancer Cell Signaling, Institute of Molecular and Cell Biology, Singapore
| | - Michael Y T Oh
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Kayoung Shin
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Jin-Ku Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Jiwon Park
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
| | - Yoon Kyung Jo
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Misuk Kim
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Vinay Tergaonkar
- Division of Cancer Cell Signaling, Institute of Molecular and Cell Biology, Singapore
- Department of Pathology, National University of Singapore, Singapore
| | - Jeongwu Lee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, Korea
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15
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Khanal T, Leung YK, Jiang W, Timchenko N, Ho SM, Kim K. NR2E3 is a key component in p53 activation by regulating a long noncoding RNA DINO in acute liver injuries. FASEB J 2019; 33:8335-8348. [PMID: 30991008 DOI: 10.1096/fj.201801881rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Damage-induced long noncoding RNA (DINO) is a long noncoding RNA that directly interacts with p53 and thereby enhances p53 stability and activity in response to various cellular stresses. Here, we demonstrate that nuclear receptor subfamily 2 group E member 3 (NR2E3) plays a crucial role in maintaining active DINO epigenetic status for its proper induction and subsequent p53 activation. In acetaminophen (APAP)- or carbon tetrachloride-induced acute liver injuries, NR2E3 knockout (KO) mice exhibited far more severe liver injuries due to impaired DINO induction and p53 activation. Mechanistically, NR2E3 loss both in vivo and in vitro induced epigenetic DINO repression accompanied by reduced DINO chromatin accessibility. Furthermore, compared with the efficient reversal by a typical antidote N-acetylcysteine (NAC) treatment of APAP-induced liver injury in wild-type mice, the liver injury of NR2E3 KO mice was not effectively reversed, indicating that an intact NR2E3-DINO-p53-signaling axis is essential for NAC-mediated recovery against APAP-induced hepatotoxicity. These findings establish that NR2E3 is a critical component in p53 activation and a novel susceptibility factor to drug- or toxicant-induced acute liver injuries.-Khanal, T., Leung, Y.-K., Jiang, W., Timchenko, N., Ho, S.-M., Kim, K. NR2E3 is a key component in p53 activation by regulating a long noncoding RNA DINO in acute liver injuries.
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Affiliation(s)
- Tilak Khanal
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Yuet-Kin Leung
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Wang Jiang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Nicolai Timchenko
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Shuk-Mei Ho
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kyounghyun Kim
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
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16
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Wang J, Shen T, Zhu W, Dou L, Gu H, Zhang L, Yang Z, Chen H, Zhou Q, Sánchez ER, Field LJ, Mayo LD, Xie Z, Xiao D, Lin X, Shou W, Yong W. Protein phosphatase 5 and the tumor suppressor p53 down-regulate each other's activities in mice. J Biol Chem 2018; 293:18218-18229. [PMID: 30262665 DOI: 10.1074/jbc.ra118.004256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/17/2018] [Indexed: 12/20/2022] Open
Abstract
Protein phosphatase 5 (PP5), a serine/threonine phosphatase, has a wide range of biological functions and exhibits elevated expression in tumor cells. We previously reported that pp5-deficient mice have altered ataxia-telangiectasia mutated (ATM)-mediated signaling and function. However, this regulation was likely indirect, as ATM is not a known PP5 substrate. In the current study, we found that pp5-deficient mice are hypersensitive to genotoxic stress. This hypersensitivity was associated with the marked up-regulation of the tumor suppressor tumor protein p53 and its downstream targets cyclin-dependent kinase inhibitor 1A (p21), MDM2 proto-oncogene (MDM2), and phosphatase and tensin homolog (PTEN) in pp5-deficient tissues and cells. These observations suggested that PP5 plays a role in regulating p53 stability and function. Experiments conducted with p53 +/- pp5 +/- or p53 +/- pp5 -/- mice revealed that complete loss of PP5 reduces tumorigenesis in the p53 +/- mice. Biochemical analyses further revealed that PP5 directly interacts with and dephosphorylates p53 at multiple serine/threonine residues, resulting in inhibition of p53-mediated transcriptional activity. Interestingly, PP5 expression was significantly up-regulated in p53-deficient cells, and further analysis of pp5 promoter activity revealed that p53 strongly represses PP5 transcription. Our results suggest a reciprocal regulatory interplay between PP5 and p53, providing an important feedback mechanism for the cellular response to genotoxic stress.
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Affiliation(s)
- Jun Wang
- From the Comparative Medical Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China,; School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Tao Shen
- DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030
| | - Wuqiang Zhu
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Longyu Dou
- From the Comparative Medical Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Hao Gu
- From the Comparative Medical Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Lingling Zhang
- From the Comparative Medical Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Zhenyun Yang
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Hanying Chen
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Qi Zhou
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Edwin R Sánchez
- Department of Physiology and Pharmacology, College of Medicine, University of Toledo, Toledo, Ohio 43614, and
| | - Loren J Field
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Lindsey D Mayo
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Zhongwen Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Deyong Xiao
- Fountain Valley Institute of Life Sciences and Fountain Valley Biomedical Technology Company, Dalian Hi-Tech Industrial Zone, Dalian 116023, China
| | - Xia Lin
- DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030
| | - Weinian Shou
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202,.
| | - Weidong Yong
- From the Comparative Medical Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China,; Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202,.
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17
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Lampreht Tratar U, Horvat S, Cemazar M. Transgenic Mouse Models in Cancer Research. Front Oncol 2018; 8:268. [PMID: 30079312 PMCID: PMC6062593 DOI: 10.3389/fonc.2018.00268] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/29/2018] [Indexed: 12/26/2022] Open
Abstract
The use of existing mouse models in cancer research is of utmost importance as they aim to explore the casual link between candidate cancer genes and carcinogenesis as well as to provide models to develop and test new therapies. However, faster progress in translating mouse cancer model research into the clinic has been hampered due to the limitations of these models to better reflect the complexities of human tumors. Traditionally, immunocompetent and immunodeficient mice with syngeneic and xenografted tumors transplanted subcutaneously or orthotopically have been used. These models are still being widely employed for many different types of studies, in part due to their widespread availability and low cost. Other types of mouse models used in cancer research comprise transgenic mice in which oncogenes can be constitutively or conditionally expressed and tumor-suppressor genes silenced using conventional methods, such as retroviral infection, microinjection of DNA constructs, and the so-called "gene-targeted transgene" approach. These traditional transgenic models have been very important in studies of carcinogenesis and tumor pathogenesis, as well as in studies evaluating the development of resistance to therapy. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing approach has revolutionized the field of mouse cancer models and has had a profound and rapid impact on the development of more effective systems to study human cancers. The CRISPR/Cas9-based transgenic models have the capacity to engineer a wide spectrum of mutations found in human cancers and provide solutions to problems that were previously unsolvable. Recently, humanized mouse xenograft models that accept patient-derived xenografts and CD34+ cells were developed to better mimic tumor heterogeneity, the tumor microenvironment, and cross-talk between the tumor and stromal/immune cells. These features make them extremely valuable models for the evaluation of investigational cancer therapies, specifically new immunotherapies. Taken together, improvements in both the CRISPR/Cas9 system producing more valid mouse models and in the humanized mouse xenograft models resembling complex interactions between the tumor and its environment might represent one of the successful pathways to precise individualized cancer therapy, leading to improved cancer patient survival and quality of life.
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Affiliation(s)
- Ursa Lampreht Tratar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Simon Horvat
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia.,Faculty of Health Sciences, University of Primorska, Isola, Slovenia
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18
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Livshits G, Alonso-Curbelo D, Morris JP, Koche R, Saborowski M, Wilkinson JE, Lowe SW. Arid1a restrains Kras-dependent changes in acinar cell identity. eLife 2018; 7:35216. [PMID: 30014851 PMCID: PMC6050044 DOI: 10.7554/elife.35216] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in members of the SWI/SNF chromatin remodeling family are common events in cancer, but the mechanisms whereby disruption of SWI/SNF components alters tumorigenesis remain poorly understood. To model the effect of loss of function mutations in the SWI/SNF subunit Arid1a in pancreatic ductal adenocarcinoma (PDAC) initiation, we directed shRNA triggered, inducible and reversible suppression of Arid1a to the mouse pancreas in the setting of oncogenic KrasG12D. Arid1a cooperates with Kras in the adult pancreas as postnatal silencing of Arid1a following sustained KrasG12D expression induces rapid and irreversible reprogramming of acinar cells into mucinous PDAC precursor lesions. In contrast, Arid1a silencing during embryogenesis, concurrent with KrasG12D activation, leads to retention of acinar cell fate. Together, our results demonstrate Arid1a as a critical modulator of Kras-dependent changes in acinar cell identity, and underscore an unanticipated influence of timing and genetic context on the effects of SWI/SNF complex alterations in epithelial tumorigenesis. The pancreas produces many different hormones, as well as several substances important for digestion. To perform these roles, the pancreas contains different types of cells; for example, acinar cells make digestive enzymes that help to break down food. But, like other cells in the body, pancreatic cells can accumulate mutations in their DNA that cause them to divide, acquire an altered identity and form a cancerous tumor. The DNA of cells is packed into a structure called chromatin. While the DNA sequence is essentially the same across all normal cells of a given individual, chromatin can be more or less compacted in the different cell types that comprise our body tissues. A collection of proteins called the SWI/SNF complex can reorganize the chromatin to change how tightly the DNA is packed. This determines which genes in the DNA are accessible and can be activated, and which ones cannot. Around 25% of pancreatic cancers contain mutations in genes that produce proteins of the SWI/SNF complex. These mutations normally occur with an additional mutation that over-activates the gene that produces a potentially cancer-causing protein called Kras. Livshits et al. have now genetically engineered mice to investigate how one such SWI/SNF complex protein, called Arid1a, affects how pancreatic cancer develops using a genetic approach that made possible to temporarily halt the production of Arid1a in acinar cells by feeding these mice an antibiotic. The gene that produces Kras was also over-activated in the pancreases of the mice, making them more likely to develop cancer. Within just two weeks of stopping the production of Arid1a, the acinar cells stopped producing digestive enzymes and started making other proteins that are typically found in cancerous cells, indicating that Arid1a is involved in maintaining the normal identity and activity of these cells. Restoring the ability of altered acinar cells to produce normal levels of Arid1a (by removing the mice from the antibiotic diet) did not reverse these changes. Biochemical experiments showed that acinar cells with reduced levels of Arid1a have altered chromatin. In particular, the genes that produce digestive enzymes, which are normally active in healthy pancreases, were less accessible in mice who had over-active Kras and reduced levels of Arid1a. The results presented by Livshits et al. provide the first evidence of how alterations to Arid1a can lead to irreversible changes in the identity and activity of pancreatic acinar cells. These results will need to be carefully considered by researchers who are developing treatments for cancer patients with mutations in Arid1a and other SWI/SNF proteins. In particular, methods that attempt to restore the functions of absent SWI/SNF proteins to cancer cells are unlikely to treat the cancer successfully.
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Affiliation(s)
- Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Direna Alonso-Curbelo
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - John P Morris
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Richard Koche
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Michael Saborowski
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, Hannover, Germany
| | - John Erby Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, United States
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, New York, United States
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19
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Rizk M, Tüzmen Ş. Update on the clinical utility of an RNA interference-based treatment: focus on Patisiran. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2017; 10:267-278. [PMID: 29184431 PMCID: PMC5689029 DOI: 10.2147/pgpm.s87945] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA interference (RNAi) is a naturally existing endogenous mechanism for post-transcriptional gene regulation, nowadays commonly utilized for functional characterization of genes and development of potential treatment strategies for diseases. RNAi-based studies for therapy, after being examined for over a decade, are finally in the pipeline for developing a potential treatment for the mutated transthyretin (TTR) gene, which gives rise to a dysfunctional TTR protein. This dysfunctional protein causes TTR amyloidosis (ATTR), an inherited, progressively incapacitating, and often fatal genetic disorder. TTR is a protein produced in the liver, and functions as a carrier for retinol-binding protein and also thyroxine. This protein facilitates the transport of vitamin A around the human body. A mutation or misprint in the code of this protein results in an abnormal folding of the protein. Therefore, not only does the transportation of the vitamin A become disabled, but also there will be formation of clusters called amyloid deposits, which attack the heart and the nerves causing some patients to be unconditionally bound to bed. ATTR is a hereditary autosomal dominant disease with a 50% chance of inheritance by offspring, even with just one of the parents having a single defective allele of this gene. Alnylam Pharmaceuticals worked on the concept of RNAi therapy for years, which led to the introduction of lipid nanoparticles encircling small interfering RNAs. The drug showed extremely positive results since the first trial, and a great percentage of defective protein reduction. This drug was later named Patisiran.
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Affiliation(s)
- Malak Rizk
- Molecular Biology and Genetics Program, Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University (EMU), Famagusta, North Cyprus, Turkey
| | - Şükrü Tüzmen
- Molecular Biology and Genetics Program, Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University (EMU), Famagusta, North Cyprus, Turkey
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20
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Kersten K, de Visser KE, van Miltenburg MH, Jonkers J. Genetically engineered mouse models in oncology research and cancer medicine. EMBO Mol Med 2017; 9:137-153. [PMID: 28028012 PMCID: PMC5286388 DOI: 10.15252/emmm.201606857] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genetically engineered mouse models (GEMMs) have contributed significantly to the field of cancer research. In contrast to cancer cell inoculation models, GEMMs develop de novo tumors in a natural immune‐proficient microenvironment. Tumors arising in advanced GEMMs closely mimic the histopathological and molecular features of their human counterparts, display genetic heterogeneity, and are able to spontaneously progress toward metastatic disease. As such, GEMMs are generally superior to cancer cell inoculation models, which show no or limited heterogeneity and are often metastatic from the start. Given that GEMMs capture both tumor cell‐intrinsic and cell‐extrinsic factors that drive de novo tumor initiation and progression toward metastatic disease, these models are indispensable for preclinical research. GEMMs have successfully been used to validate candidate cancer genes and drug targets, assess therapy efficacy, dissect the impact of the tumor microenvironment, and evaluate mechanisms of drug resistance. In vivo validation of candidate cancer genes and therapeutic targets is further accelerated by recent advances in genetic engineering that enable fast‐track generation and fine‐tuning of GEMMs to more closely resemble human patients. In addition, aligning preclinical tumor intervention studies in advanced GEMMs with clinical studies in patients is expected to accelerate the development of novel therapeutic strategies and their translation into the clinic.
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Affiliation(s)
- Kelly Kersten
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin E de Visser
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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21
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Kastenhuber ER, Lowe SW. Putting p53 in Context. Cell 2017; 170:1062-1078. [PMID: 28886379 DOI: 10.1016/j.cell.2017.08.028] [Citation(s) in RCA: 1370] [Impact Index Per Article: 171.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/09/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. Functionally, p53 is activated by a host of stress stimuli and, in turn, governs an exquisitely complex anti-proliferative transcriptional program that touches upon a bewildering array of biological responses. Despite the many unveiled facets of the p53 network, a clear appreciation of how and in what contexts p53 exerts its diverse effects remains unclear. How can we interpret p53's disparate activities and the consequences of its dysfunction to understand how cell type, mutation profile, and epigenetic cell state dictate outcomes, and how might we restore its tumor-suppressive activities in cancer?
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Affiliation(s)
- Edward R Kastenhuber
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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22
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Kato M, Huang YY, Matsuo M, Takashina Y, Sasaki K, Horai Y, Juni A, Kamijo SI, Saigo K, Ui-Tei K, Tei H. RNAi-mediated knockdown of mouse melanocortin-4 receptor in vitro and in vivo, using an siRNA expression construct based on the mir-187 precursor. Exp Anim 2017; 66:41-50. [PMID: 27725374 PMCID: PMC5301000 DOI: 10.1538/expanim.16-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool for the study of gene function in mammalian
systems, including transgenic mice. Here, we report a gene knockdown system based on the
human mir-187 precursor. We introduced small interfering RNA (siRNA) sequences against the
mouse melanocortin-4 receptor (mMc4r) to alter the targeting of miR-187.
The siRNA-expressing cassette was placed under the control of the cytomegalovirus (CMV)
early enhancer/chicken β-actin promoter. In vitro, the construct
efficiently knocked down the gene expression of a co-transfected
mMc4r-expression vector in cultured mammalian cells. Using this
construct, we generated a transgenic mouse line which exhibited partial but significant
knockdown of mMc4r mRNA in various brain regions. Northern blot analysis
detected transgenic expression of mMc4r siRNA in these regions.
Furthermore, the transgenic mice fed a normal diet ate 9% more and were 30% heavier than
wild-type sibs. They also developed hyperinsulinemia and fatty liver as do
mMc4r knockout mice. We determined that this siRNA expression construct
based on mir-187 is a practical and useful tool for gene functional studies in
vitro as well as in vivo.
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Affiliation(s)
- Minoru Kato
- Research Unit/Neuroscience, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
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23
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Manchado E, Huang CH, Tasdemir N, Tschaharganeh DF, Wilkinson JE, Lowe SW. A Pipeline for Drug Target Identification and Validation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 81:257-267. [PMID: 28057848 PMCID: PMC5469697 DOI: 10.1101/sqb.2016.81.031096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rapid and affordable tumor profiling has led to an explosion of genomic data that is facilitating the development of new cancer therapies. The potential of therapeutic strategies aimed at inactivating the oncogenic lesions that contribute to the aberrant survival and proliferation of tumor cells has yielded remarkable success in some malignancies such as BRAF-mutant melanoma and BCR-ABL expressing chronic myeloid leukemia. However, the direct inhibition of several well-established oncoproteins in some of these cancers is not possible or produces only transient benefits. Functional genomics represents a powerful approach for the identification of vulnerabilities linked to specific genetic alterations and has provided substantial insights into cancer signaling networks. Still, as inhibition of gene function can have diverse effects on both tumor and normal tissues, information on the potency of target inhibition on tumor growth as well as the toxic side effects of target inhibition are also needed. Here, we discuss our RNA interference (RNAi) pipeline for cancer target discovery based on our optimized short-hairpin RNA (shRNA) tools for negative selection screens and inducible RNAi platform that, in combination with embryonic stem cell (ESC)-based genetically engineered mouse models (GEMMs), enable deep in vivo target validation.
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Affiliation(s)
- Eusebio Manchado
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065
| | - Nilgun Tasdemir
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - John E Wilkinson
- ULAM/Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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24
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Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet 2016; 48:1370-1376. [PMID: 27668660 PMCID: PMC5083181 DOI: 10.1038/ng.3673] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022]
Abstract
Long noncoding RNAs (lncRNAs) are prevalent genes with frequently precise regulation but mostly unknown functions. Here we demonstrate that lncRNAs guide the organismal DNA damage response. DNA damage activated transcription of the DINO (Damage Induced Noncoding) lncRNA via p53. DINO was required for p53-dependent gene expression, cell cycle arrest and apoptosis in response to DNA damage, and DINO expression was sufficient to activate damage signaling and cell cycle arrest in the absence of DNA damage. DINO bound to p53 protein and promoted its stabilization, mediating a p53 auto-amplification loop. Dino knockout or promoter inactivation in mice dampened p53 signaling and ameliorated acute radiation syndrome in vivo. Thus, inducible lncRNA can create a feedback loop with its cognate transcription factor to amplify cellular signaling networks.
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Affiliation(s)
- Adam M Schmitt
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Julia T Garcia
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Tiffany Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Kun Qu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Y Payumo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ashwin Peres-da-Silva
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | | | - Rachel Baum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shuling Guo
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
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25
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Tschaharganeh DF, Lowe SW, Garippa RJ, Livshits G. Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J 2016; 283:3194-203. [PMID: 27149548 DOI: 10.1111/febs.13750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 12/23/2022]
Abstract
The recent discovery of the CRISPR/Cas system and repurposing of this technology to edit a variety of different genomes have revolutionized an array of scientific fields, from genetics and translational research, to agriculture and bioproduction. In particular, the prospect of rapid and precise genome editing in laboratory animals by CRISPR/Cas has generated an immense interest in the scientific community. Here we review current in vivo applications of CRISPR/Cas and how this technology can improve our knowledge of gene function and our understanding of biological processes in animal models.
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Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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26
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Recombinase-based conditional and reversible gene regulation via XTR alleles. Nat Commun 2015; 6:8783. [PMID: 26537451 PMCID: PMC4635517 DOI: 10.1038/ncomms9783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/30/2015] [Indexed: 01/28/2023] Open
Abstract
Synthetic biological tools that enable precise regulation of gene function within in vivo systems have enormous potential to discern gene function in diverse physiological settings. Here we report the development and characterization of a synthetic gene switch that, when targeted in the mouse germline, enables conditional inactivation, reports gene expression and allows inducible restoration of the targeted gene. Gene inactivation and reporter expression is achieved through Cre-mediated stable inversion of an integrated gene-trap reporter, whereas inducible gene restoration is afforded by Flp-dependent deletion of the inverted gene trap. We validate our approach by targeting the p53 and Rb genes and establishing cell line and in vivo cancer model systems, to study the impact of p53 or Rb inactivation and restoration. We term this allele system XTR, to denote each of the allelic states and the associated expression patterns of the targeted gene: eXpressed (XTR), Trapped (TR) and Restored (R).
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27
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Hemann M. Chimeric Tumor and Organ Transplantation Models. Cold Spring Harb Protoc 2015; 2015:725-30. [PMID: 26240412 DOI: 10.1101/pdb.top069872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mouse models of cancer development and progression provide a means to study tumor response in appropriate physiological contexts. However, mouse cancer progression and therapy models have traditionally suffered from many of the same problems as human clinical cancer research, including genetic heterogeneity and tumor-stage variability at the time of treatment. Additionally, most mouse models are not tractable genetic systems, making it difficult to recapitulate the diverse set of alterations that regularly occur during tumor development. The recent development of chimeric and tumor transplantation techniques address many of the limitations of conventional mouse genetics. These strategies allow for the somatic introduction of complex genetic alterations into a subset of cells in reconstituted tumors or organ systems. Moreover, these different approaches can be combined in such a way that tumors with multiple genotypes are rapidly produced. These matched pairs can be systemically introduced into recipient mice for the rapid ex vivo modification of preestablished malignancies allows the generation of "matched pairs" of tumors differing in a single defined lesion (i.e., aliquots of the same primary malignancy with and without a gene of interest). Thus, treatment studies can be performed (1) in the context of an otherwise normal organ system, (2) on tumors that are in their appropriate anatomical context, and (3) on tumors that are essentially identical besides the presence of defined experimentally introduced alterations. Here, we will introduce procedures for modifying both normal and transformed cells and their adaptation to study in vivo tumor biology.
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Affiliation(s)
- Michael Hemann
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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28
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Cooperative loss of RAS feedback regulation drives myeloid leukemogenesis. Nat Genet 2015; 47:539-43. [PMID: 25822087 PMCID: PMC4414804 DOI: 10.1038/ng.3251] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/24/2015] [Indexed: 01/15/2023]
Abstract
RAS network activation is common in human cancers and, in acute myeloid leukemia (AML), achieved mainly through gain-of-function mutations in KRAS, NRAS, or the FLT3 receptor tyrosine kinase1. In mice, we show that premalignant myeloid cells harboring a KrasG12D allele retain low Ras signaling owing to a negative feedback involving Spry4 that prevents transformation. In humans, SPRY4 is located on chromosome 5q, a region affected by large heterozygous deletion that are associated with an aggressive disease in which gain-of-function RAS pathway mutations are rare. These 5q deletions often co-occur with chromosome 17 alterations involving deletion of NF1 - another RAS negative regulator - and TP53. Accordingly, combined suppression of Spry4, Nf1 and Trp53 produces high Ras signaling and drives AML in mice. Therefore, SPRY4 is a 5q tumor suppressor whose disruption contributes to a lethal AML subtype that appears to acquire RAS pathway activation through loss of negative regulators.
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29
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Rytlewski JA, Beronja S. RNAi in the mouse: rapid and affordable gene function studies in a vertebrate system. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2014; 4:45-57. [DOI: 10.1002/wdev.164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/29/2014] [Accepted: 10/15/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Julie A. Rytlewski
- Human Biology Division; Fred Hutchinson Cancer Research Center; Seattle WA USA
| | - Slobodan Beronja
- Human Biology Division; Fred Hutchinson Cancer Research Center; Seattle WA USA
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30
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Huang CH, Lujambio A, Zuber J, Tschaharganeh DF, Doran MG, Evans MJ, Kitzing T, Zhu N, de Stanchina E, Sawyers CL, Armstrong SA, Lewis JS, Sherr CJ, Lowe SW. CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. Genes Dev 2014; 28:1800-14. [PMID: 25128497 PMCID: PMC4197965 DOI: 10.1101/gad.244368.114] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One-year survival rates for newly diagnosed hepatocellular carcinoma (HCC) are <50%, and unresectable HCC carries a dismal prognosis owing to its aggressiveness and the undruggable nature of its main genetic drivers. By screening a custom library of shRNAs directed toward known drug targets in a genetically defined Myc-driven HCC model, we identified cyclin-dependent kinase 9 (Cdk9) as required for disease maintenance. Pharmacological or shRNA-mediated CDK9 inhibition led to robust anti-tumor effects that correlated with MYC expression levels and depended on the role that both CDK9 and MYC exert in transcription elongation. Our results establish CDK9 inhibition as a therapeutic strategy for MYC-overexpressing liver tumors and highlight the relevance of transcription elongation in the addiction of cancer cells to MYC.
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Affiliation(s)
- Chun-Hao Huang
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Amaia Lujambio
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Johannes Zuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | | | - Michael G Doran
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Michael J Evans
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Thomas Kitzing
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nan Zhu
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | | | - Charles L Sawyers
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Scott A Armstrong
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jason S Lewis
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Charles J Sherr
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Scott W Lowe
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;
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Thom CS, Traxler EA, Khandros E, Nickas JM, Zhou OY, Lazarus JE, Silva APG, Prabhu D, Yao Y, Aribeana C, Fuchs SY, Mackay JP, Holzbaur ELF, Weiss MJ. Trim58 degrades Dynein and regulates terminal erythropoiesis. Dev Cell 2014; 30:688-700. [PMID: 25241935 DOI: 10.1016/j.devcel.2014.07.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 04/24/2014] [Accepted: 07/28/2014] [Indexed: 01/23/2023]
Abstract
TRIM58 is an E3 ubiquitin ligase superfamily member implicated by genome-wide association studies to regulate human erythrocyte traits. Here, we show that Trim58 expression is induced during late erythropoiesis and that its depletion by small hairpin RNAs (shRNAs) inhibits the maturation of late-stage nucleated erythroblasts to anucleate reticulocytes. Imaging flow cytometry studies demonstrate that Trim58 regulates polarization and/or extrusion of erythroblast nuclei. In vitro, Trim58 directly binds and ubiquitinates the intermediate chain of the microtubule motor dynein. In cells, Trim58 stimulates proteasome-dependent degradation of the dynein holoprotein complex. During erythropoiesis, Trim58 expression, dynein loss, and enucleation occur concomitantly, and all are inhibited by Trim58 shRNAs. Dynein regulates nuclear positioning and microtubule organization, both of which undergo dramatic changes during erythroblast enucleation. Thus, we propose that Trim58 promotes this process by eliminating dynein. Our findings identify an erythroid-specific regulator of enucleation and elucidate a previously unrecognized mechanism for controlling dynein activity.
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Affiliation(s)
- Christopher S Thom
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Traxler
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenna M Nickas
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Olivia Y Zhou
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacob E Lazarus
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Dolly Prabhu
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Yao
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chiaka Aribeana
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Serge Y Fuchs
- Department of Animal Biology and Mari Lowe Comparative Oncology Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Erika L F Holzbaur
- Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell J Weiss
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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Mansoori B, Sandoghchian Shotorbani S, Baradaran B. RNA interference and its role in cancer therapy. Adv Pharm Bull 2014; 4:313-21. [PMID: 25436185 DOI: 10.5681/apb.2014.046] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/16/2014] [Accepted: 04/19/2014] [Indexed: 12/21/2022] Open
Abstract
In todays' environment, it is becoming increasingly difficult to ignore the role of cancer in social health. Although a huge budget is allocated on cancer research every year, cancer remains the second global cause of death. And, exclusively, less than 50% of patients afflicted with advanced cancer live one year subsequent to standard cancer treatments. RNA interference (RNAi) is a mechanism for gene silencing. Such mechanism possesses uncanny ability in targeting cancer-related genes. A majority of gene products involved in tumorigenesis have recently been utilized as targets in RNAi based therapy. The evidence from these studies indicates that RNAi application for targeting functional carcinogenic molecules, tumor resistance to chemotherapy and radiotherapy is required in today's cancer treatment. Knock downing of gene products by RNAi technology exerts antiproliferative and proapoptotic effects upon cell culture systems, animal models and in clinical trials in the most studies. The recognition of RNAi mechanism and the progress in this field leaded several new RNAi-based drugs to Clinical Trial phases. This has also developed genome based personalized cancer therapeutics. Hopefully, this type of treatment will work as one of the efficient one for cancer patients.
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Affiliation(s)
- Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Micklem DR, Blø M, Bergström P, Hodneland E, Tiron C, Høiby T, Gjerdrum C, Hammarsten O, Lorens JB. Flow cytometry-based functional selection of RNA interference triggers for efficient epi-allelic analysis of therapeutic targets. BMC Biotechnol 2014; 14:57. [PMID: 24952598 PMCID: PMC4074332 DOI: 10.1186/1472-6750-14-57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/18/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The dose-response relationship is a fundamental pharmacological parameter necessary to determine therapeutic thresholds. Epi-allelic hypomorphic analysis using RNA interference (RNAi) can similarly correlate target gene dosage with cellular phenotypes. This however requires a set of RNAi triggers empirically determined to attenuate target gene expression to different levels. RESULTS In order to improve our ability to incorporate epi-allelic analysis into target validation studies, we developed a novel flow cytometry-based functional screening approach (CellSelectRNAi) to achieve unbiased selection of shRNAs from high-coverage libraries that knockdown target gene expression to predetermined levels. Employing a Gaussian probability model we calculated that knockdown efficiency is inferred from shRNA sequence frequency profiles derived from sorted hypomorphic cell populations. We used this approach to generate a hypomorphic epi-allelic cell series of shRNAs to reveal a functional threshold for the tumor suppressor p53 in normal and transformed cells. CONCLUSION The unbiased CellSelectRNAi flow cytometry-based functional screening approach readily provides an epi-allelic series of shRNAs for graded reduction of target gene expression and improved phenotypic validation.
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Affiliation(s)
- David R Micklem
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
- BerGenBio A/S, N-5009, Bergen, Norway
| | - Magnus Blø
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
- BerGenBio A/S, N-5009, Bergen, Norway
| | - Petra Bergström
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, S-413 45 Göteborg, Sweden
| | - Erlend Hodneland
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Crina Tiron
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Torill Høiby
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | | | - Ola Hammarsten
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, S-413 45 Göteborg, Sweden
| | - James B Lorens
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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Hwang HW, Baxter LL, Loftus SK, Cronin JC, Trivedi NS, Borate B, Pavan WJ. Distinct microRNA expression signatures are associated with melanoma subtypes and are regulated by HIF1A. Pigment Cell Melanoma Res 2014; 27:777-87. [PMID: 24767210 DOI: 10.1111/pcmr.12255] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/24/2014] [Indexed: 01/23/2023]
Abstract
The complex genetic changes underlying metastatic melanoma need to be deciphered to develop new and effective therapeutics. Previously, genome-wide microarray analyses of human melanoma identified two reciprocal gene expression programs, including transcripts regulated by either transforming growth factor, beta 1 (TGFβ1) pathways, or microphthalmia-associated transcription factor (MITF)/SRY-box containing gene 10 (SOX10) pathways. We extended this knowledge by discovering that melanoma cell lines with these two expression programs exhibit distinctive microRNA (miRNA) expression patterns. We also demonstrated that hypoxia-inducible factor 1 alpha (HIF1A) is increased in TGFβ1 pathway-expressing melanoma cells and that HIF1A upregulates miR-210, miR-218, miR-224, and miR-452. Reduced expression of these four miRNAs in TGFβ1 pathway-expressing melanoma cells arrests the cell cycle, while their overexpression in mouse melanoma cells increases the expression of the hypoxic response gene Bnip3. Taken together, these data suggest that HIF1A may regulate some of the gene expression and biological behavior of TGFβ1 pathway-expressing melanoma cells, in part via alterations in these four miRNAs.
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Affiliation(s)
- Hun-Way Hwang
- Genetic Disease Research Branch, Department of Health and Human Services, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Weissmueller S, Manchado E, Saborowski M, Morris JP, Wagenblast E, Davis CA, Moon SH, Pfister NT, Tschaharganeh DF, Kitzing T, Aust D, Markert EK, Wu J, Grimmond SM, Pilarsky C, Prives C, Biankin AV, Lowe SW. Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling. Cell 2014; 157:382-394. [PMID: 24725405 PMCID: PMC4001090 DOI: 10.1016/j.cell.2014.01.066] [Citation(s) in RCA: 402] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/17/2013] [Accepted: 01/23/2014] [Indexed: 12/14/2022]
Abstract
Missense mutations in the p53 tumor suppressor inactivate its antiproliferative properties but can also promote metastasis through a gain-of-function activity. We show that sustained expression of mutant p53 is required to maintain the prometastatic phenotype of a murine model of pancreatic cancer, a highly metastatic disease that frequently displays p53 mutations. Transcriptional profiling and functional screening identified the platelet-derived growth factor receptor b (PDGFRb) as both necessary and sufficient to mediate these effects. Mutant p53 induced PDGFRb through a cell-autonomous mechanism involving inhibition of a p73/NF-Y complex that represses PDGFRb expression in p53-deficient, noninvasive cells. Blocking PDGFRb signaling by RNA interference or by small molecule inhibitors prevented pancreatic cancer cell invasion in vitro and metastasis formation in vivo. Finally, high PDGFRb expression correlates with poor disease-free survival in pancreatic, colon, and ovarian cancer patients, implicating PDGFRb as a prognostic marker and possible target for attenuating metastasis in p53 mutant tumors.
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Affiliation(s)
- Susann Weissmueller
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eusebio Manchado
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Saborowski
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - John P Morris
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Elvin Wagenblast
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Carrie A Davis
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sung-Hwan Moon
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Neil T Pfister
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Kitzing
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Daniela Aust
- Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, 01062 Dresden, Germany
| | - Elke K Markert
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
| | - Jianmin Wu
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Sean M Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Santa Lucia 4072, Australia; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland G61 1BD, UK
| | - Christian Pilarsky
- Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, 01062 Dresden, Germany
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Andrew V Biankin
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland G61 1BD, UK
| | - Scott W Lowe
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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36
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Abstract
RNA interference has become an indispensable tool for loss-of-function studies across eukaryotes. By enabling stable and reversible gene silencing, shRNAs provide a means to study long-term phenotypes, perform pool-based forward genetic screens and examine the consequences of temporary target inhibition in vivo. However, efficient implementation in vertebrate systems has been hindered by technical difficulties affecting potency and specificity. Focusing on these issues, we analyse current strategies to obtain maximal knockdown with minimal off-target effects.
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37
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Abstract
Saborowski et al. developed a flexible embryonic stem cell (ESC)-based mouse model for pancreatic cancer. The ESCs harbor a latent Kras mutant, a homing cassette, and other genetic elements needed for rapid insertion and conditional expression of tetracycline-controlled transgenes, including fluorescence-coupled shRNAs. This model produces a disease that follows the progression of human pancreatic cancer, and they used it to dissect temporal roles for Pten and c-Myc in pancreatic cancer development and maintenance. Genetically engineered mouse models (GEMMs) have greatly expanded our knowledge of pancreatic ductal adenocarcinoma (PDAC) and serve as a critical tool to identify and evaluate new treatment strategies. However, the cost and time required to generate conventional pancreatic cancer GEMMs limits their use for investigating novel genetic interactions in tumor development and maintenance. To address this problem, we developed flexible embryonic stem cell (ESC)-based GEMMs that facilitate the rapid generation of genetically defined multiallelic chimeric mice without further strain intercrossing. The ESCs harbor a latent Kras mutant (a nearly ubiquitous feature of pancreatic cancer), a homing cassette, and other genetic elements needed for rapid insertion and conditional expression of tetracycline-controlled transgenes, including fluorescence-coupled shRNAs capable of efficiently silencing gene function by RNAi. This system produces a disease that recapitulates the progression of pancreatic cancer in human patients and enables the study and visualization of the impact of gene perturbation at any stage of pancreas cancer progression. We describe the use of this approach to dissect temporal roles for the tumor suppressor Pten and the oncogene c-Myc in pancreatic cancer development and maintenance.
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RNAi-mediated knockdown of IKK1 in transgenic mice using a transgenic construct containing the human H1 promoter. ScientificWorldJournal 2014; 2014:193803. [PMID: 24523631 PMCID: PMC3913291 DOI: 10.1155/2014/193803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/12/2013] [Indexed: 01/16/2023] Open
Abstract
Inhibition of gene expression through siRNAs is a tool increasingly used for the study of gene function in model systems, including transgenic mice. To achieve perdurable effects, the stable expression of siRNAs by an integrated transgenic construct is necessary. For transgenic siRNA expression, promoters transcribed by either RNApol II or III (such as U6 or H1 promoters) can be used. Relatively large amounts of small RNAs synthesis are achieved when using RNApol III promoters, which can be advantageous in knockdown experiments. To study the feasibility of H1 promoter-driven RNAi-expressing constructs for protein knockdown in transgenic mice, we chose IKK1 as the target gene. Our results indicate that constructs containing the H1 promoter are sensitive to the presence of prokaryotic sequences and to transgene position effects, similar to RNApol II promoters-driven constructs. We observed variable expression levels of transgenic siRNA among different tissues and animals and a reduction of up to 80% in IKK1 expression. Furthermore, IKK1 knockdown led to hair follicle alterations. In summary, we show that constructs directed by the H1 promoter can be used for knockdown of genes of interest in different organs and for the generation of animal models complementary to knockout and overexpression models.
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39
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Kim J, Badaloni A, Willert T, Zimber-Strobl U, Kühn R, Wurst W, Kieslinger M. An RNAi-based approach to down-regulate a gene family in vivo. PLoS One 2013; 8:e80312. [PMID: 24265806 PMCID: PMC3827190 DOI: 10.1371/journal.pone.0080312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022] Open
Abstract
Genetic redundancy poses a major problem to the analysis of gene function. RNA interference allows the down-regulation of several genes simultaneously, offering the possibility to overcome genetic redundancy, something not easily achieved with traditional genetic approaches. Previously we have used a polycistronic miR155-based framework to knockdown expression of three genes of the early B cell factor family in cultured cells. Here we develop the system further by generating transgenic mice expressing the RNAi construct in vivo in an inducible manner. Expression of the transgene from the strong CAG promoter is compatible with a normal function of the basal miRNA/RNAi machinery, and the miR155 framework readily allows inducible expression from the Rosa26 locus as shown by Gfp. However, expression of the transgene in hematopoietic cells does not lead to changes in B cell development and neuronal expression does not affect cerebellar architecture as predicted from genetic deletion studies. Protein as well as mRNA levels generated from Ebf genes in hetero- and homozygous animals are comparable to wild-type levels. A likely explanation for the discrepancy in the effectiveness of the RNAi construct between cultured cells and transgenic animals lies in the efficiency of the sequences used, possibly together with the complexity of the transgene. Since new approaches allow to overcome efficiency problems of RNAi sequences, the data lay the foundation for future work on the simultaneous knockdown of several genes in vivo.
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Affiliation(s)
- Jeehee Kim
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Aurora Badaloni
- Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Torsten Willert
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ursula Zimber-Strobl
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Matthias Kieslinger
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- * E-mail:
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40
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Livshits G, Lowe SW. Accelerating cancer modeling with RNAi and nongermline genetically engineered mouse models. Cold Spring Harb Protoc 2013; 2013:2013/11/pdb.top069856. [PMID: 24184755 DOI: 10.1101/pdb.top069856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
For more than two decades, genetically engineered mouse models have been key to our mechanistic understanding of tumorigenesis and cancer progression. Recently, the massive quantity of data emerging from cancer genomics studies has demanded a corresponding increase in the efficiency and throughput of in vivo models for functional testing of putative cancer genes. Already a mainstay of cancer research, recent innovations in RNA interference (RNAi) technology have extended its utility for studying gene function and genetic interactions, enabling tissue-specific, inducible and reversible gene silencing in vivo. Concurrent advances in embryonic stem cell (ESC) culture and genome engineering have accelerated several steps of genetically engineered mouse model production and have facilitated the incorporation of RNAi technology into these models. Here, we review the current state of these technologies and examine how their integration has the potential to dramatically enhance the throughput and capabilities of animal models for cancer.
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Affiliation(s)
- Geulah Livshits
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065
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41
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Olive V, Sabio E, Bennett MJ, De Jong CS, Biton A, McGann JC, Greaney SK, Sodir NM, Zhou AY, Balakrishnan A, Foth M, Luftig MA, Goga A, Speed TP, Xuan Z, Evan GI, Wan Y, Minella AC, He L. A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis. eLife 2013; 2:e00822. [PMID: 24137534 PMCID: PMC3796314 DOI: 10.7554/elife.00822] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/12/2013] [Indexed: 12/15/2022] Open
Abstract
mir-17-92, a potent polycistronic oncomir, encodes six mature miRNAs with complex modes of interactions. In the Eμ-myc Burkitt’s lymphoma model, mir-17-92 exhibits potent oncogenic activity by repressing c-Myc-induced apoptosis, primarily through its miR-19 components. Surprisingly, mir-17-92 also encodes the miR-92 component that negatively regulates its oncogenic cooperation with c-Myc. This miR-92 effect is, at least in part, mediated by its direct repression of Fbw7, which promotes the proteosomal degradation of c-Myc. Thus, overexpressing miR-92 leads to aberrant c-Myc increase, imposing a strong coupling between excessive proliferation and p53-dependent apoptosis. Interestingly, miR-92 antagonizes the oncogenic miR-19 miRNAs; and such functional interaction coordinates proliferation and apoptosis during c-Myc-induced oncogenesis. This miR-19:miR-92 antagonism is disrupted in B-lymphoma cells that favor a greater increase of miR-19 over miR-92. Altogether, we suggest a new paradigm whereby the unique gene structure of a polycistronic oncomir confers an intricate balance between oncogene and tumor suppressor crosstalk. DOI:http://dx.doi.org/10.7554/eLife.00822.001 The role of genes, in very simple terms, is to be transcribed into messenger RNA molecules, which are then translated into strings of amino acids that fold into proteins. Each of these steps is extremely complex, and a wide range of other molecules can speed up, slow down, stop or otherwise disrupt the expression of genes as protein products. Genes can also code for nucleic acids that are not translated into proteins, such as microRNAs. These are small RNA molecules that can reduce the production of proteins by repressing the translation step and/or by partially degrading the messenger RNA molecules. mir-17-92 is a gene that exemplifies much of this complexity. It codes for six different microRNAs in a single primary transcript, and has been implicated in a number of cancers, including lung cancer, Burkitt’s lymphoma and other forms of lymphomas and leukemia. One of six microRNAs has a longer evolutionary history than the remaining five: mir-92 is found in vertebrates, chordates and invertebrates, whereas the other five are only found in vertebrates. However, it is not known how or why the mir-17-92 gene evolved to code for multiple different microRNAs. Olive et al. have studied how these mir-17-92 microRNAs functionally interact in mice with Burkitt’s lymphoma, a form of cancer that is associated with a gene called c-Myc being over-activated. Mutations in this gene promote the proliferation of cells, and in cooperation with other genetic lesions, this ultimately leads to cancer. mir-17-92 is implicated in this cancer because it represses the process of programmed cell death (which is induced by the protein c-Myc) that the body employs to stop tumors growing. Olive et al. found that deleting one of the six microRNAs, miR-92, increased the tendency of the mir-17-92 gene to promote Burkitt’s lymphoma. By repressing an enzyme called Fbw7, miR-92 causes high levels of c-Myc to be produced. While this leads to the uncontrolled proliferation of cells that promotes cancer, it also increases programmed cell death, at least in part, by activating the p53 pathway, a well-known tumor suppression pathway. The experiments also revealed that the action of miR-92 and that of one of the other microRNAs, miR-19, were often opposed to each other. These findings have revealed an unexpected interaction among different components within a single microRNA gene, which acts to maintain an intricate balance between pathways that promote and suppress cancer. DOI:http://dx.doi.org/10.7554/eLife.00822.002
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Affiliation(s)
- Virginie Olive
- Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States
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Budina-Kolomets A, Hontz RD, Pimkina J, Murphy ME. A conserved domain in exon 2 coding for the human and murine ARF tumor suppressor protein is required for autophagy induction. Autophagy 2013; 9:1553-65. [PMID: 23939042 PMCID: PMC4623555 DOI: 10.4161/auto.25831] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 01/25/2023] Open
Abstract
The ARF tumor suppressor, encoded by the CDKN2A gene, has a well-defined role regulating TP53 stability; this activity maps to exon 1β of CDKN2A. In contrast, little is known about the function(s) of exon 2 of ARF, which contains the majority of mutations in human cancer. In addition to controlling TP53 stability, ARF also has a role in the induction of autophagy. However, whether the principal molecule involved is full-length ARF, or a small molecular weight variant called smARF, has been controversial. Additionally, whether tumor-derived mutations in exon 2 of CDKN2A affect ARF's autophagy function is unknown. Finally, whereas it is known that silencing or inhibiting TP53 induces autophagy, the contribution of ARF to this induction is unknown. In this report we used multiple autophagy assays to map a region located in the highly conserved 5' end of exon 2 of CDKN2A that is necessary for autophagy induction by both human and murine ARF. We showed that mutations in exon 2 of CDKN2A that affect the coding potential of ARF, but not p16INK4a, all impair the ability of ARF to induce autophagy. We showed that whereas full-length ARF can induce autophagy, our combined data suggest that smARF instead induces mitophagy (selective autophagy of mitochondria), thus potentially resolving some confusion regarding the role of these variants. Finally, we showed that silencing Tp53 induces autophagy in an ARF-dependent manner. Our data indicated that a conserved domain in ARF mediates autophagy, and for the first time they implicate autophagy in ARF's tumor suppressor function.
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Affiliation(s)
- Anna Budina-Kolomets
- Program in Molecular and Cellular Oncogenesis; Wistar Institute; Philadelphia, PA USA
| | - Robert D Hontz
- Program in Molecular and Cellular Oncogenesis; Wistar Institute; Philadelphia, PA USA
| | - Julia Pimkina
- Program in Molecular and Cellular Oncogenesis; Wistar Institute; Philadelphia, PA USA
| | - Maureen E Murphy
- Program in Molecular and Cellular Oncogenesis; Wistar Institute; Philadelphia, PA USA
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Yang RF, Zhao GW, Liang ST, Chen HZ, Liu DP. Lysine-specific demethylase 1 represses THP-1 monocyte-to-macrophage differentiation. ACTA ACUST UNITED AC 2013; 28:82-7. [PMID: 23806369 DOI: 10.1016/s1001-9294(13)60027-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To investigate the role of lysine-specific demethylase 1 (LSD1) in the process of THP-1 monocyte-to-macrophage differentiation. METHODS Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blotting were performed to analyze the expression of LSD1 and interleukin-6 (IL-6) in THP-1 monocytes and THP-1-derived macrophages. Chromatin immunoprecipitation (ChIP) assay was applied to detect the occupancy of LSD1 and H3K4 methylation at IL-6 promoter during THP-1 monocyte-to-macrophage differentiation. IL-6 mRNA level and H3K4 methylation at IL-6 promoter were analyzed using qRT-PCR and ChIP assay in LSD1-knockdown THP-1 cells treated with 12-O-tetradecanoylphorbol-13-acetate (TPA) for 0, 4, 8, 12, and 24 hours. Fluorescence activated flow cytometry was performed to reveal the percentage of macrophages differentiated from THP-1 monocytes. RESULTS The expression of LSD1 reduced during THP-1 monocyte-to-macrophage differentiation (P<0.01). LSD1 occupancy decreased and H3K4 methylation increased at IL-6 promoter during the differentiation. With knockdown of LSD1, H3K4 methylation at IL-6 promoter was found increased after TPA treatment at different times points (all P<0.05, except 24 hours). The percentage of macrophages increased significantly in the THP-1 cells with LSD1 knockdown (P<0.05). CONCLUSIONS LSD1 is repressed during the monocyte-to-macrophage differentiation of THP-1 cells. Suppression of LSD1-mediated H3K4 demethylation may be required for THP-1 monocyte-to-macrophage differentiation.
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Affiliation(s)
- Rui-feng Yang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
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Kawakami Y, Ii M, Matsumoto T, Kawamoto A, Kuroda R, Akimaru H, Mifune Y, Shoji T, Fukui T, Asahi M, Kurosaka M, Asahara T. A small interfering RNA targeting Lnk accelerates bone fracture healing with early neovascularization. J Transl Med 2013; 93:1036-53. [PMID: 23897412 DOI: 10.1038/labinvest.2013.93] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/03/2013] [Accepted: 07/07/2013] [Indexed: 12/14/2022] Open
Abstract
Lnk, an intracellular adapter protein, is expressed in hematopoietic cell lineages, which has recently been proved as an essential inhibitory signaling molecule for stem cell self-renewal in the stem cell factor-c-Kit signaling pathway with enhanced hematopoietic and osteogenic reconstitution in Lnk-deficient mice. Moreover, the therapeutic potential of hematopoietic stem/endothelial progenitor cells (EPCs) for fracture healing has been demonstrated with mechanistic insight into vasculogenesis/angiogenesis and osteogenesis enhancement in the fracture sites. We report here, Lnk siRNA-transfected endothelial commitment of c-kit+/Sca-1+/lineage- subpopulations of bone marrow cells have high EPC colony-forming capacity exhibiting endothelial markers, VE-Cad, VEGF and Ang-1. Lnk siRNA-transfected osteoblasts also show highly osteoblastic capacity. In vivo, locally transfected Lnk siRNA could successfully downregulate the expression of Lnk at the fracture site up to 1 week, and radiological and histological examination showed extremely accelerated fracture healing in Lnk siRNA-transfected mice. Moreover, Lnk siRNA-transfected mice exhibited sufficient therapeutic outcomes with intrinstic enhancement of angiogenesis and osteogenesis, specifically, the mice demonstrated better blood flow recovery in the sites of fracture. In our series of experiments, we clarified that a negatively regulated Lnk system contributed to a favorable circumstance for fracture healing by enhancing vasculogenesis/angiogenesis and osteogenesis. These findings suggest that downregulation of Lnk system may have the clinical potential for faster fracture healing, which contributes to the reduction of delayed unions or non-unions.
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Affiliation(s)
- Yohei Kawakami
- Group of Vascular Regeneration, Institute of Biomedical Research and Innovation, Kobe, Japan
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45
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Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA. Integrated network analyses for functional genomic studies in cancer. Semin Cancer Biol 2013; 23:213-8. [PMID: 23811269 DOI: 10.1016/j.semcancer.2013.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 11/24/2022]
Abstract
RNA-interference (RNAi) studies hold great promise for functional investigation of the significance of genetic variations and mutations, as well as potential synthetic lethalities, for understanding and treatment of cancer, yet technical and conceptual issues currently diminish the potential power of this approach. While numerous research groups are usefully employing this kind of functional genomic methodology to identify molecular mediators of disease severity, response, and resistance to treatment, findings are generally confounded by "off-target" effects. These effects arise from a variety of issues beyond non-specific reagent behavior, such as biological cross-talk and feedback processes so thus can occur even with specific perturbation. Interpreting RNAi results in a network framework instead of merely as individual "hits" or "targets" leverages contributions from all hit/target contributions to pathways via their relationships with other network nodes. This interpretation can ameliorate dependence upon individual reagent performance and increase confidence in biological validation. Here we provide background on RNAi studies in cancer applications, review key challenges with functional genomics, and motivate the use of network models grounded in pathway analyses.
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Affiliation(s)
- Jennifer L Wilson
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.
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46
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van der Weyden L, Adams DJ. Cancer of mice and men: old twists and new tails. J Pathol 2013; 230:4-16. [PMID: 23436574 DOI: 10.1002/path.4184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 01/28/2013] [Accepted: 02/16/2013] [Indexed: 12/18/2022]
Abstract
In this review we set out to celebrate the contribution that mouse models of human cancer have made to our understanding of the fundamental mechanisms driving tumourigenesis. We take the opportunity to look forward to how the mouse will be used to model cancer and the tools and technologies that will be applied, and indulge in looking back at the key advances the mouse has made possible.
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47
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Synthetic microRNA-mediated downregulation of Nogo-A in transgenic rats reveals its role as regulator of synaptic plasticity and cognitive function. Proc Natl Acad Sci U S A 2013; 110:6583-8. [PMID: 23576723 DOI: 10.1073/pnas.1217665110] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We have generated a transgenic rat model using RNAi and used it to study the role of the membrane protein Nogo-A in synaptic plasticity and cognition. The membrane protein Nogo-A is expressed in CNS oligodendrocytes and subpopulations of neurons, and it is known to suppress neurite growth and regeneration. The constitutively expressed polymerase II-driven transgene was composed of a microRNA-targeting Nogo-A placed into an intron preceding the coding sequence for EGFP, thus quantitatively labeling cells according to intracellular microRNA expression. The transgenic microRNA in vivo efficiently reduced the concentration of Nogo-A mRNA and protein preferentially in neurons. The resulting significant increase in long-term potentiation in both hippocampus and motor cortex indicates a repressor function of Nogo-A in synaptic plasticity. The transgenic rats exhibited prominent schizophrenia-like behavioral phenotypes, such as perseveration, disrupted prepulse inhibition, and strong withdrawal from social interactions. This fast and efficient microRNA-mediated knockdown provides a way to silence gene expression in vivo in transgenic rats and shows a role of Nogo-A in regulating higher cognitive brain functions.
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48
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Hu S, Ni W, Sai W, Zi H, Qiao J, Wang P, Sheng J, Chen C. Knockdown of myostatin expression by RNAi enhances muscle growth in transgenic sheep. PLoS One 2013; 8:e58521. [PMID: 23526994 PMCID: PMC3603981 DOI: 10.1371/journal.pone.0058521] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
Myostatin (MSTN) has been shown to be a negative regulator of skeletal muscle development and growth. MSTN dysfunction therefore offers a strategy for promoting animal growth performance in livestock production. In this study, we investigated the possibility of using RNAi-based technology to generate transgenic sheep with a double-muscle phenotype. A shRNA expression cassette targeting sheep MSTN was used to generate stable shRNA-expressing fibroblast clones. Transgenic sheep were further produced by somatic cell nuclear transfer (SCNT) technology. Five lambs developed to term and three live lambs were obtained. Integration of shRNA expression cassette in three live lambs was confirmed by PCR. RNase protection assay showed that the shRNAs targeting MSTN were expressed in muscle tissues of three transgenic sheep. MSTN expression was significantly inhibited in muscle tissues of transgenic sheep when compared with control sheep. Moreover, transgenic sheep showed a tendency to faster increase in body weight than control sheep. Histological analysis showed that myofiber diameter of transgenic sheep M17 were bigger than that of control sheep. Our findings demonstrate a promising approach to promoting muscle growth in livestock production.
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Affiliation(s)
- Shengwei Hu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, China
| | - Wujiafu Sai
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Ha Zi
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Pengyang Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jinliang Sheng
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, China
- * E-mail:
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González F, Georgieva D, Vanoli F, Shi ZD, Stadtfeld M, Ludwig T, Jasin M, Huangfu D. Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. Cell Rep 2013; 3:651-60. [PMID: 23478019 DOI: 10.1016/j.celrep.2013.02.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/15/2013] [Accepted: 02/04/2013] [Indexed: 12/17/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great promise for personalized regenerative medicine. However, recent studies show that iPSC lines carry genetic abnormalities, suggesting that reprogramming may be mutagenic. Here, we show that the ectopic expression of reprogramming factors increases the level of phosphorylated histone H2AX, one of the earliest cellular responses to DNA double-strand breaks (DSBs). Additional mechanistic studies uncover a direct role of the homologous recombination (HR) pathway, a pathway essential for error-free repair of DNA DSBs, in reprogramming. This role is independent of the use of integrative or nonintegrative methods in introducing reprogramming factors, despite the latter being considered a safer approach that circumvents genetic modifications. Finally, deletion of the tumor suppressor p53 rescues the reprogramming phenotype in HR-deficient cells primarily through the restoration of reprogramming-dependent defects in cell proliferation and apoptosis. These mechanistic insights have important implications for the design of safer approaches to creating iPSCs.
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Affiliation(s)
- Federico González
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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50
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Yin D, Ogawa S, Kawamata N, Leiter A, Ham M, Li D, Doan NB, Said JW, Black KL, Phillip Koeffler H. miR-34a functions as a tumor suppressor modulating EGFR in glioblastoma multiforme. Oncogene 2013; 32:1155-1163. [PMID: 22580610 PMCID: PMC4085050 DOI: 10.1038/onc.2012.132] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 02/24/2012] [Accepted: 03/07/2012] [Indexed: 12/13/2022]
Abstract
Chromosome 1p36.23 is frequently deleted in glioblastoma multiforme (GBM). miR-34a localizes in this region. Our experiments found that miR-34a was often deleted and epidermal growth factor receptor (EGFR) was frequently amplified in genomic DNA of 55 GBMs using single-nucleotide polymorphism DNA microarray. Notably, we found that the mean survival time was significantly shortened for patients whose GBMs had both EGFR amplification and miR-34a deletion. Expression of miR-34a was significantly lower in GBM samples compared with normal brain tissue. Forced expression of miR-34a in GBM cells decreased their ability to migrate and profoundly decreased their levels of cyclin-A1, -B1, -D1, and -D3, as well as cyclin-dependent kinase and increased expression of cyclin kinase inhibitor proteins (p21, p27). Also, human GBM cells (U251) stable overexpressing mir-34a formed smaller tumors when growing as xenografts in immunodeficient mice compared with wild-type U251 GBM cells. Furthermore, the protein expression of EGFR decreased in the cells with forced overexpression of miR-34a. Additional studies showed that mir-34a targeted Yin Yang-1 (YY1) and YY1 is a transcription factor that can stimulate the expression of EGFR. Thus, our data suggest that miR-34a acts as a tumor suppressor by inhibiting growth of GBM cells in vitro and in vivo associated with moderating the expression of cell-cycle proteins and EGFR. Moreover, we discovered for the first time that both deletion of miR-34a and amplification of EGFR were associated with significantly decreased overall survival of GBM patients.
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Affiliation(s)
- D Yin
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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