1
|
Behrouzian Fard G, Ahmadi MH, Gholamin M, Amirfakhrian R, Saberi Teimourian E, Karimi MA, Hosseini Bafghi M. CRISPR-Cas9 technology: As an efficient genome modification tool in the cancer diagnosis and treatment. Biotechnol Bioeng 2024; 121:472-488. [PMID: 37986642 DOI: 10.1002/bit.28603] [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: 08/01/2023] [Revised: 09/30/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Cancer is the second most common cause of death globally and is a major public health concern. Managing this disease is difficult due to its multiple stages and numerous genetic and epigenetic changes. Traditional cancer diagnosis and treatment methods have limitations, making it crucial to develop new modalities to combat the increasing burden of cancer. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has transformed genetic engineering due to its simplicity, specificity, low cytotoxicity, and cost-effectiveness. It has been proposed as an effective technology to enhance cancer diagnosis and treatment strategies. This article presents the most recent discoveries regarding the structure, mechanism, and delivery methods of the highly powerful genome editing tool, CRISPR-Cas9. In terms of diagnosis, the article examines the role of CRISPR-Cas9 in detecting microRNAs and DNA methylation, and discusses two popular gene detection techniques that utilize the CRISPR-Cas system: DNA endonuclease-targeted CRISPR trans reporter and specific high sensitivity enzymatic reporter unlocking. Regarding treatment, the article explores several genes that have been identified and modified by CRISPR-Cas9 for effective tumorigenesis of common cancers such as breast, lung, and colorectal cancer. The present review also addresses the challenges and ethical issues associated with using CRISPR-Cas9 as a diagnostic and therapeutic tool. Despite some limitations, CRISPR-Cas9-based cancer diagnosis has the potential to become the next generation of cancer diagnostic tools, and the continuous progress of CRISPR-Cas9 can greatly aid in cancer treatment.
Collapse
Affiliation(s)
- Ghazaleh Behrouzian Fard
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hossein Ahmadi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehran Gholamin
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Razieh Amirfakhrian
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Saberi Teimourian
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ali Karimi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdi Hosseini Bafghi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
2
|
Yang Z, Zhang Z, Li J, Chen W, Liu C. CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system. Brief Bioinform 2024; 25:bbae066. [PMID: 38426328 PMCID: PMC10905519 DOI: 10.1093/bib/bbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
CRISPR/Cas9 is a promising RNA-guided genome editing technology, which consists of a Cas9 nuclease and a single-guide RNA (sgRNA). So far, a number of sgRNA prediction softwares have been developed. However, they were usually designed for protein-coding genes without considering that long non-coding RNA (lncRNA) genes may have different characteristics. In this study, we first evaluated the performances of a series of known sgRNA-designing tools in the context of both coding and non-coding datasets. Meanwhile, we analyzed the underpinnings of their varied performances on the sgRNA's specificity for lncRNA including nucleic acid sequence, genome location and editing mechanism preference. Furthermore, we introduce a support vector machine-based machine learning algorithm named CRISPRlnc, which aims to model both CRISPR knock-out (CRISPRko) and CRISPR inhibition (CRISPRi) mechanisms to predict the on-target activity of targets. CRISPRlnc combined the paired-sgRNA design and off-target analysis to achieve one-stop design of CRISPR/Cas9 sgRNAs for non-coding genes. Performance comparison on multiple datasets showed that CRISPRlnc was far superior to existing methods for both CRISPRko and CRISPRi mechanisms during the lncRNA-specific sgRNA design. To maximize the availability of CRISPRlnc, we developed a web server (http://predict.crisprlnc.cc) and made it available for download on GitHub.
Collapse
Affiliation(s)
- Zitian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zexin Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Chen
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, School of Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
3
|
Shen W, Hu F, Lei P, Tang Y. Applications of CRISPR screening to lung cancer treatment. Front Cell Dev Biol 2023; 11:1295555. [PMID: 38169973 PMCID: PMC10760454 DOI: 10.3389/fcell.2023.1295555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Lung cancer is an extremely aggressive and highly prevalent disease worldwide, and it is one of the leading causes of cancer death. Deciphering intrinsic genetic mechanism, finding new targets, and overcoming drug resistance are the key to lung cancer treatment. High-throughput CRISPR screening has been extensively used to obtain the genes related to cancers including lung cancer. This review describes CRISPR/Cas9 or CRISPR/dCas9-based technologies for high-throughput screening. We summarize the applications of CRISPR screening technology in exploring the mechanism of lung cancer development in vivo or in vitro, overcoming drug resistance, improving the effect of immunotherapy, and discovering new therapeutic targets. This review highlights the potential of CRISPR screening in combination with tumor barcoding and high-throughput sequencing (Tuba-seq) to precisely quantify the impact of alterations in many tumor suppressor genes on lung cancer.
Collapse
Affiliation(s)
- Wanying Shen
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Fangli Hu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Pan Lei
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
- Hubei Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yijun Tang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
4
|
García-Caballero D, Hart JR, Vogt PK. Long Non-Coding RNAs as "MYC Facilitators". PATHOPHYSIOLOGY 2023; 30:389-399. [PMID: 37755396 PMCID: PMC10534484 DOI: 10.3390/pathophysiology30030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
In this article, we discuss a class of MYC-interacting lncRNAs (long non-coding RNAs) that share the following criteria: They are direct transcriptional targets of MYC. Their expression is coordinated with the expression of MYC. They are required for sustained MYC-driven cell proliferation, and they are not essential for cell survival. We refer to these lncRNAs as "MYC facilitators" and discuss two representative members of this class of lncRNAs, SNHG17 (small nuclear RNA host gene) and LNROP (long non-coding regulator of POU2F2). We also present a general hypothesis on the role of lncRNAs in MYC-mediated transcriptional regulation.
Collapse
Affiliation(s)
| | | | - Peter K. Vogt
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| |
Collapse
|
5
|
García-Caballero D, Hart JR, Vogt PK. The MYC-regulated lncRNA LNROP (ENSG00000254887) enables MYC-driven cell proliferation by controlling the expression of OCT2. Cell Death Dis 2023; 14:168. [PMID: 36849510 PMCID: PMC9971199 DOI: 10.1038/s41419-023-05683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023]
Abstract
MYC controls most of the non-coding genome. Several long noncoding transcripts were originally identified in the human B cell line P496-3 and then shown to be required for MYC-driven proliferation of Burkitt lymphoma-derived RAMOS cells. In this study, we used RAMOS cells exclusively as a representative of the human B cell lineage. One of the MYC-controlled lncRNAs required for RAMOS cell proliferation is ENSG00000254887 which we will term LNROP (long non-coding regulator of POU2F2). In the genome, LNROP is located in close proximity of POU2F2, the gene encoding OCT2. OCT2 is a transcription factor with important roles in sustaining the proliferation of human B cells. Here we show that LNROP is a nuclear RNA and a direct target of MYC. Downregulation of LNROP attenuates the expression of OCT2. This effect of LNROP on the expression of OCT2 is unidirectional as downregulation of OCT2 does not alter the expression of LNROP. Our data suggest that LNROP is a cis-acting regulator of OCT2. To illustrate the downstream reach of LNROP, we chose a prominent target of OCT2, the tyrosine phosphatase SHP-1. Downregulation of OCT2 elevates the expression of SHP-1. Our data suggest the following path of interactions: LNROP enables the proliferation of B cells by positively and unidirectionally regulating the growth-stimulatory transcription factor OCT2. In actively proliferating B cells, OCT2 attenuates the expression and anti-proliferative activity of SHP-1.
Collapse
Affiliation(s)
- Daniel García-Caballero
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Jonathan R Hart
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter K Vogt
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| |
Collapse
|
6
|
Xu L, Sun B, Liu S, Gao X, Zhou H, Li F, Li Y. The evaluation of active transcriptional repressor domain for CRISPRi in plants. Gene 2023; 851:146967. [DOI: 10.1016/j.gene.2022.146967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/20/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
|
7
|
Weber LI, Hartl M. Strategies to target the cancer driver MYC in tumor cells. Front Oncol 2023; 13:1142111. [PMID: 36969025 PMCID: PMC10032378 DOI: 10.3389/fonc.2023.1142111] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/10/2023] [Indexed: 03/29/2023] Open
Abstract
The MYC oncoprotein functions as a master regulator of cellular transcription and executes non-transcriptional tasks relevant to DNA replication and cell cycle regulation, thereby interacting with multiple proteins. MYC is required for fundamental cellular processes triggering proliferation, growth, differentiation, or apoptosis and also represents a major cancer driver being aberrantly activated in most human tumors. Due to its non-enzymatic biochemical functions and largely unstructured surface, MYC has remained difficult for specific inhibitor compounds to directly address, and consequently, alternative approaches leading to indirect MYC inhibition have evolved. Nowadays, multiple organic compounds, nucleic acids, or peptides specifically interfering with MYC activities are in preclinical or early-stage clinical studies, but none of them have been approved so far for the pharmacological treatment of cancer patients. In addition, specific and efficient delivery technologies to deliver MYC-inhibiting agents into MYC-dependent tumor cells are just beginning to emerge. In this review, an overview of direct and indirect MYC-inhibiting agents and their modes of MYC inhibition is given. Furthermore, we summarize current possibilities to deliver appropriate drugs into cancer cells containing derailed MYC using viral vectors or appropriate nanoparticles. Finding the right formulation to target MYC-dependent cancers and to achieve a high intracellular concentration of compounds blocking or attenuating oncogenic MYC activities could be as important as the development of novel MYC-inhibiting principles.
Collapse
|
8
|
Mills C, Riching A, Keller A, Stombaugh J, Haupt A, Maksimova E, Dickerson SM, Anderson E, Hemphill K, Ebmeier C, Schiel JA, Levenga J, Perkett M, Smith AVB, Strezoska Z. A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs. CRISPR J 2022; 5:769-786. [PMID: 36257604 PMCID: PMC9805873 DOI: 10.1089/crispr.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/15/2022] [Indexed: 01/31/2023] Open
Abstract
While CRISPR interference (CRISPRi) systems have been widely implemented in pooled lentiviral screening, there has been limited use with synthetic guide RNAs for the complex phenotypic readouts enabled by experiments in arrayed format. Here we describe a novel deactivated Cas9 fusion protein, dCas9-SALL1-SDS3, which produces greater target gene repression than first or second generation CRISPRi systems when used with chemically modified synthetic single guide RNAs (sgRNAs), while exhibiting high target specificity. We show that dCas9-SALL1-SDS3 interacts with key members of the histone deacetylase and Swi-independent three complexes, which are the endogenous functional effectors of SALL1 and SDS3. Synthetic sgRNAs can also be used with in vitro-transcribed dCas9-SALL1-SDS3 mRNA for short-term delivery into primary cells, including human induced pluripotent stem cells and primary T cells. Finally, we used dCas9-SALL1-SDS3 for functional gene characterization of DNA damage host factors, orthogonally to small interfering RNA, demonstrating the ability of the system to be used in arrayed-format screening.
Collapse
Affiliation(s)
- Clarence Mills
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Andrew Riching
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Ashleigh Keller
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Jesse Stombaugh
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Amanda Haupt
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Elena Maksimova
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Sarah M. Dickerson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Emily Anderson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Kevin Hemphill
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Chris Ebmeier
- Mass Spectrometry Core Facility, University of Colorado-Boulder, Boulder, Colorado, USA
| | - John A. Schiel
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Josien Levenga
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Matthew Perkett
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Anja van Brabant Smith
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Zaklina Strezoska
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| |
Collapse
|
9
|
Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
Collapse
Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| |
Collapse
|
10
|
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: 18] [Impact Index Per Article: 9.0] [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.
Collapse
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.
| |
Collapse
|
11
|
Replogle JM, Bonnar JL, Pogson AN, Liem CR, Maier NK, Ding Y, Russell BJ, Wang X, Leng K, Guna A, Norman TM, Pak RA, Ramos DM, Ward ME, Gilbert LA, Kampmann M, Weissman JS, Jost M. Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors. eLife 2022; 11:81856. [PMID: 36576240 PMCID: PMC9829409 DOI: 10.7554/elife.81856] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
CRISPR interference (CRISPRi) enables programmable, reversible, and titratable repression of gene expression (knockdown) in mammalian cells. Initial CRISPRi-mediated genetic screens have showcased the potential to address basic questions in cell biology, genetics, and biotechnology, but wider deployment of CRISPRi screening has been constrained by the large size of single guide RNA (sgRNA) libraries and challenges in generating cell models with consistent CRISPRi-mediated knockdown. Here, we present next-generation CRISPRi sgRNA libraries and effector expression constructs that enable strong and consistent knockdown across mammalian cell models. First, we combine empirical sgRNA selection with a dual-sgRNA library design to generate an ultra-compact (1-3 elements per gene), highly active CRISPRi sgRNA library. Next, we compare CRISPRi effectors to show that the recently published Zim3-dCas9 provides an excellent balance between strong on-target knockdown and minimal non-specific effects on cell growth or the transcriptome. Finally, we engineer a suite of cell lines with stable expression of Zim3-dCas9 and robust on-target knockdown. Our results and publicly available reagents establish best practices for CRISPRi genetic screening.
Collapse
Affiliation(s)
- Joseph M Replogle
- Medical Scientist Training Program, University of California, San FranciscoSan FranciscoUnited States,Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Jessica L Bonnar
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Christina R Liem
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Nolan K Maier
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Yufang Ding
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Baylee J Russell
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Xingren Wang
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Kun Leng
- Medical Scientist Training Program, University of California, San FranciscoSan FranciscoUnited States,Institute for Neurodegenerative Disease, University of California, San FranciscoSan FranciscoUnited States
| | - Alina Guna
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Ryan A Pak
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel M Ramos
- Center for Alzheimer's Disease and Related Dementias, National Institutes of HealthBethesdaUnited States,National Institute on Aging, National Institutes of HealthBethesdaUnited States
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaUnited States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States,Arc InstitutePalo AltoUnited States
| | - Martin Kampmann
- Institute for Neurodegenerative Disease, University of California, San FranciscoSan FranciscoUnited States,Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States,Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Department of Microbiology, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
12
|
miRNA- and lncRNA-Based Therapeutics for Non-Hodgkin’s Lymphoma: Moving towards an RNA-Guided Precision Medicine. Cancers (Basel) 2021; 13:cancers13246324. [PMID: 34944942 PMCID: PMC8699447 DOI: 10.3390/cancers13246324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Non-Hodgkin’s lymphoma (NHL) is a very heterogenous class of hematological cancers, with variable patient outcomes. Therefore, there is an urgent need to develop new and more effective therapeutic approaches. MiRNAs and lncRNAs have emerged as the central gene expression regulators, and their deregulation has been reported to be involved in lymphomagenesis. Given their ability to simultaneously modulate multiple targets, they provide an attractive therapeutic approach to treat NHL patients. In this review, we discuss the scientific rationale behind miRNA/lncRNA-based therapies in NHL and the different targeting technologies, such as antisense oligonucleotides, CRISPR-Cas9, and nanomedicines. Abstract Increasing evidence has demonstrated the functional roles of miRNAs and lncRNAs in lymphoma onset and progression, either by acting as tumor-promoting ncRNAs or as tumor suppressors, emphasizing their appeal as lymphoma therapeutics. In fact, their intrinsic ability to modulate multiple dysregulated genes and/or signaling pathways makes them an attractive therapeutic approach for a multifactorial pathology like lymphoma. Currently, the clinical application of miRNA- and lncRNA-based therapies still faces obstacles regarding effective delivery systems, off-target effects, and safety, which can be minimized with the appropriate chemical modifications and the development of tumor site-specific delivery approaches. Moreover, miRNA- and lncRNA-based therapeutics are being studied not only as monotherapies but also as complements of standard treatment regimens to provide a synergic effect, improving the overall treatment efficacy and reducing the therapeutic resistance. In this review, we summarize the fundamentals of miRNA- and lncRNA-based therapeutics by discussing the different types of delivery systems, with a focus on those that have been investigated in lymphoma in vitro and in vivo. Moreover, we described the ongoing clinical trials of novel miRNA- and lncRNA-based therapeutics in lymphoma.
Collapse
|
13
|
Hazan J, Bester AC. CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs. Noncoding RNA 2021; 7:79. [PMID: 34940760 PMCID: PMC8704461 DOI: 10.3390/ncrna7040079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022] Open
Abstract
Over the last decade, tens of thousands of new long non-coding RNAs (lncRNAs) have been identified in the human genome. Nevertheless, except for a handful of genes, the genetic characteristics and functions of most of these lncRNAs remain elusive; this is partially due to their relatively low expression, high tissue specificity, and low conservation across species. A major limitation for determining the function of lncRNAs was the lack of methodologies suitable for studying these genes. The recent development of CRISPR/Cas9 technology has opened unprecedented opportunities to uncover the genetic and functional characteristics of the non-coding genome via targeted and high-throughput approaches. Specific CRISPR/Cas9-based approaches were developed to target lncRNA loci. Some of these approaches involve modifying the sequence, but others were developed to study lncRNAs by inducing transcriptional and epigenetic changes. The discovery of other programable Cas proteins broaden our possibilities to target RNA molecules with greater precision and accuracy. These approaches allow for the knock-down and characterization of lncRNAs. Here, we review how various CRISPR-based strategies have been used to characterize lncRNAs with important functions in different biological contexts and how these approaches can be further utilized to improve our understanding of the non-coding genome.
Collapse
|
14
|
S. Zibitt M, Hartford CCR, Lal A. Interrogating lncRNA functions via CRISPR/Cas systems. RNA Biol 2021; 18:2097-2106. [PMID: 33685382 PMCID: PMC8632070 DOI: 10.1080/15476286.2021.1899500] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are an increasing focus of investigation due to their implications in diverse biological processes and disease. Nevertheless, the majority of lncRNAs are low in abundance and poorly conserved, posing challenges to functional studies. The CRISPR/Cas system, an innovative technology that has emerged over the last decade, can be utilized to further understand lncRNA function. The system targets specific DNA and/or RNA sequences via a guide RNA (gRNA) and Cas nuclease complex. We and others have utilized this technology in various applications such as lncRNA knockout, knockdown, overexpression, and imaging. In this review, we summarize how the CRISPR/Cas technology provides new tools to investigate the roles and therapeutic implications of lncRNAs.
Collapse
Affiliation(s)
- Meira S. Zibitt
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Corrine Corrina R. Hartford
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| |
Collapse
|
15
|
Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, Liu X, Lv Z, Yang P, Xu W, Gao W, Wu Y. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol Cancer 2021; 20:126. [PMID: 34598686 PMCID: PMC8484294 DOI: 10.1186/s12943-021-01431-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.
Collapse
Affiliation(s)
- Huimin Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Chunhong Qin
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Changming An
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Shuxin Wen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Wenjie Chen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Xianfang Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Zhenghua Lv
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Pingchang Yang
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, 518055, Guangdong, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, 518055, Guangdong, China
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China. .,Department of Cell biology and Genetics, Basic Medical School of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China.
| |
Collapse
|
16
|
Hegre SA, Samdal H, Klima A, Stovner EB, Nørsett KG, Liabakk NB, Olsen LC, Chawla K, Aas PA, Sætrom P. Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation. Sci Rep 2021; 11:18952. [PMID: 34556693 PMCID: PMC8460802 DOI: 10.1038/s41598-021-97909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/26/2021] [Indexed: 11/09/2022] Open
Abstract
Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 57 lncRNAs. We selected four of these lncRNAs-SNHG26, EMSLR, ZFAS1, and EPB41L4A-AS1-for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.
Collapse
Affiliation(s)
- Siv Anita Hegre
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Helle Samdal
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Antonin Klima
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Endre B Stovner
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Kristin G Nørsett
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Nina Beate Liabakk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Lene Christin Olsen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,The Central Norway Regional Health Authority, St. Olavs Hospital HF, Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
| |
Collapse
|
17
|
Liaño-Pons J, Arsenian-Henriksson M, León J. The Multiple Faces of MNT and Its Role as a MYC Modulator. Cancers (Basel) 2021; 13:4682. [PMID: 34572909 PMCID: PMC8465425 DOI: 10.3390/cancers13184682] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/29/2022] Open
Abstract
MNT is a crucial modulator of MYC, controls several cellular functions, and is activated in most human cancers. It is the largest, most divergent, and most ubiquitously expressed protein of the MXD family. MNT was first described as a MYC antagonist and tumor suppressor. Indeed, 10% of human tumors present deletions of one MNT allele. However, some reports show that MNT functions in cooperation with MYC by maintaining cell proliferation, promoting tumor cell survival, and supporting MYC-driven tumorigenesis in cellular and animal models. Although MAX was originally considered MNT's obligate partner, our recent findings demonstrate that MNT also works independently. MNT forms homodimers and interacts with proteins both outside and inside of the proximal MYC network. These complexes are involved in a wide array of cellular processes, from transcriptional repression via SIN3 to the modulation of metabolism through MLX as well as immunity and apoptosis via REL. In this review, we discuss the present knowledge of MNT with a special focus on its interactome, which sheds light on the complex and essential role of MNT in cell biology.
Collapse
Affiliation(s)
- Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden;
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden;
| | - Javier León
- Departmento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain;
| |
Collapse
|
18
|
DiStefano JK, Gerhard GS. Long Noncoding RNAs and Human Liver Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:1-21. [PMID: 34416820 DOI: 10.1146/annurev-pathol-042320-115255] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Johanna K DiStefano
- Diabetes and Fibrotic Disease Research Unit, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA;
| | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA;
| |
Collapse
|
19
|
Nakamura M, Ivec AE, Gao Y, Qi LS. Durable CRISPR-Based Epigenetic Silencing. BIODESIGN RESEARCH 2021; 2021:9815820. [PMID: 37849948 PMCID: PMC10521745 DOI: 10.34133/2021/9815820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/28/2021] [Indexed: 10/19/2023] Open
Abstract
Development of CRISPR-based epigenome editing tools is important for the study and engineering of biological behavior. Here, we describe the design of a reporter system for quantifying the ability of CRISPR epigenome editors to produce a stable gene repression. We characterize the dynamics of durable gene silencing and reactivation, as well as the induced epigenetic changes of this system. We report the creation of single-protein CRISPR constructs bearing combinations of three epigenetic editing domains, termed KAL, that can stably repress the gene expression. This system should allow for the development of novel epigenome editing tools which will be useful in a wide array of biological research and engineering applications.
Collapse
Affiliation(s)
| | - Alexis E. Ivec
- Department of Bioengineering, Stanford, CA 94305USA
- Program in Human Biology, Stanford, CA 94305USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford, CA 94305USA
- Cancer Biology Program, Stanford, CA 94305USA
| | - Lei S. Qi
- Department of Bioengineering, Stanford, CA 94305USA
- Department of Chemical and Systems Biology, Stanford, CA 94305USA
- ChEM-H Institute, Stanford, CA 94305USA
| |
Collapse
|
20
|
Horodecka K, Düchler M. CRISPR/Cas9: Principle, Applications, and Delivery through Extracellular Vesicles. Int J Mol Sci 2021; 22:6072. [PMID: 34199901 PMCID: PMC8200053 DOI: 10.3390/ijms22116072] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/20/2022] Open
Abstract
The establishment of CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) technology for eukaryotic gene editing opened up new avenues not only for the analysis of gene function but also for therapeutic interventions. While the original methodology allowed for targeted gene disruption, recent technological advancements yielded a rich assortment of tools to modify genes and gene expression in various ways. Currently, clinical applications of this technology fell short of expectations mainly due to problems with the efficient and safe delivery of CRISPR/Cas9 components to living organisms. The targeted in vivo delivery of therapeutic nucleic acids and proteins remain technically challenging and further limitations emerge, for instance, by unwanted off-target effects, immune reactions, toxicity, or rapid degradation of the transfer vehicles. One approach that might overcome many of these limitations employs extracellular vesicles as intercellular delivery devices. In this review, we first introduce the CRISPR/Cas9 system and its latest advancements, outline major applications, and summarize the current state of the art technology using exosomes or microvesicles for transporting CRISPR/Cas9 constituents into eukaryotic cells.
Collapse
Affiliation(s)
| | - Markus Düchler
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 112 Sienkiewicza Street, 90-363 Lodz, Poland;
| |
Collapse
|
21
|
Wang M, Dai M, Wang D, Tang T, Xiong F, Xiang B, Zhou M, Li X, Li Y, Xiong W, Li G, Zeng Z, Guo C. The long noncoding RNA AATBC promotes breast cancer migration and invasion by interacting with YBX1 and activating the YAP1/Hippo signaling pathway. Cancer Lett 2021; 512:60-72. [PMID: 33951538 DOI: 10.1016/j.canlet.2021.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) play an important role in the regulation of gene expression and are involved in several pathological responses. However, many important lncRNAs in breast cancer have not been identified and their expression levels and functions in breast cancer remain unknown. In this study, the lncRNA apoptosis-associated transcript in bladder cancer (AATBC) was found to be significantly highly expressed in breast cancer patients. In vitro and in vivo experiments indicated that AATBC promoted breast cancer metastasis. Further studies revealed that AATBC activated the YAP1/Hippo signaling pathway through the AATBC-YBX1-MST1 axis. This is also an important supplement to the composition of the YAP1/Hippo signaling pathway. The model of "AATBC-YAP1" may bring a new dawn to the treatment of breast cancer.
Collapse
Affiliation(s)
- Maonan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Manli Dai
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ting Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Fang Xiong
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yong Li
- Department of Medicine, Comprehensive Cancer Center Baylor College of Medicine, Houston, TX, USA
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
22
|
Nakamura M, Gao Y, Dominguez AA, Qi LS. CRISPR technologies for precise epigenome editing. Nat Cell Biol 2021; 23:11-22. [PMID: 33420494 DOI: 10.1038/s41556-020-00620-7] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.
Collapse
Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Cancer Biology Program, Stanford University, Stanford, CA, USA.,Mammoth Biosciences, South San Francisco, CA, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Sana Biotechnology, South San Francisco, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA. .,Stanford ChEM-H Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
23
|
Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer. Cancers (Basel) 2020; 12:cancers12123695. [PMID: 33317042 PMCID: PMC7763270 DOI: 10.3390/cancers12123695] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Long non-coding RNAs (lncRNAs) are a recently discovered class of molecules in the cell, with potential to be utilized as therapeutic targets in cancer. A number of lncRNAs have been described to play important roles in tumor progression and drive molecular processes involved in cell proliferation, apoptosis or invasion. However, the vast majority of lncRNAs have not been studied in the context of cancer thus far. With the advent of CRISPR/Cas genome editing, high-throughput functional screening approaches to identify lncRNAs that impact cancer growth are becoming more accessible. Here, we review currently available methods to study hundreds to thousands of lncRNAs in parallel to elucidate their role in tumorigenesis and cancer progression. Abstract Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.
Collapse
|
24
|
Li R, Xia X, Wang X, Sun X, Dai Z, Huo D, Zheng H, Xiong H, He A, Wu X. Generation and validation of versatile inducible CRISPRi embryonic stem cell and mouse model. PLoS Biol 2020; 18:e3000749. [PMID: 33253175 PMCID: PMC7728392 DOI: 10.1371/journal.pbio.3000749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 12/10/2020] [Accepted: 11/02/2020] [Indexed: 01/09/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) 9 has been widely used far beyond genome editing. Fusions of deactivated Cas9 (dCas9) to transcription effectors enable interrogation of the epigenome and controlling of gene expression. However, the large transgene size of dCas9-fusion hinders its applications especially in somatic tissues. Here, we develop a robust CRISPR interference (CRISPRi) system by transgenic expression of doxycycline (Dox) inducible dCas9-KRAB in mouse embryonic stem cells (iKRAB ESC). After introduction of specific single-guide RNAs (sgRNAs), the induced dCas9-KRAB efficiently maintains gene inactivation, although it modestly down-regulates the expression of active genes. The proper timing of Dox addition during cell differentiation or reprogramming allows us to study or screen spatiotemporally activated promoters or enhancers and thereby the gene functions. Furthermore, taking the ESC for blastocyst injection, we generate an iKRAB knock-in (KI) mouse model that enables the shutdown of gene expression and loss-of-function (LOF) studies ex vivo and in vivo by a simple transduction of gRNAs. Thus, our inducible CRISPRi ESC line and KI mouse provide versatile and convenient platforms for functional interrogation and high-throughput screens of specific genes and potential regulatory elements in the setting of development or diseases.
Collapse
Affiliation(s)
- Rui Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianyou Xia
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xing Wang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Sun
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhongye Dai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dawei Huo
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Huimin Zheng
- Department of Prosthodontics, School and Hospital of Stomatology, Tianjin Medical University, Tianjin, China
| | - Haiqing Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin, China
| |
Collapse
|
25
|
Tu R, Chen Z, Bao Q, Liu H, Qing G. Crosstalk between oncogenic MYC and noncoding RNAs in cancer. Semin Cancer Biol 2020; 75:62-71. [DOI: 10.1016/j.semcancer.2020.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 12/19/2022]
|
26
|
Xue VW, Wong SCC, Cho WCS. Genome-wide CRISPR screens for the identification of therapeutic targets for cancer treatment. Expert Opin Ther Targets 2020; 24:1147-1158. [PMID: 32893711 DOI: 10.1080/14728222.2020.1820986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Exploring the function of every gene is a challenging task. There is a paradigm shift of RNA interference with the introduction of clustered regularly interspaced short palindromic repeat (CRISPR)-based genome-wide screening. CRISPR-based screening can detect the loss-of-function and gain-of-function targets. Many DNA-binding proteins are engineered as effective tools for modulating gene expression and for investigating therapeutic targets for a spectrum of diseases. Among them, CRISPR-Cas9 has received extensive attention with its potential for screening cancer treatment targets. AREAS COVERED This article reviews CRISPR toolkit and its applications in screening cancer therapeutic targets, especially genome-wide screens using different CRISPR-Cas9 systems. We compare and summarize the characteristics of CRISPR systems, which would be helpful for understanding and optimizing current CRISPR toolkits, as well as reflecting on the potential future development and clinical applications of CRISPR screens. EXPERT OPINION The application of CRISPR-based therapeutic target screening is broadly used in cancer drug development. Its application in cancer immunotherapy and precision oncology is blooming. Nevertheless, more effective methods of Cas protein delivery and the development of more accurate and efficient genome-editing tools are needed.
Collapse
Affiliation(s)
- Vivian Weiwen Xue
- Department of Anatomical and Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong , Hong Kong, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University , Hong Kong, China
| | | |
Collapse
|
27
|
Phelan JD, Staudt LM. CRISPR-based technology to silence the expression of IncRNAs. Proc Natl Acad Sci U S A 2020; 117:8225-8227. [PMID: 32245807 PMCID: PMC7165436 DOI: 10.1073/pnas.2003702117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
28
|
Raffeiner P, Hart JR, García-Caballero D, Bar-Peled L, Weinberg MS, Vogt PK. An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation. Proc Natl Acad Sci U S A 2020; 117:6571-6579. [PMID: 32156728 PMCID: PMC7104257 DOI: 10.1073/pnas.1921786117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MYC controls the transcription of large numbers of long noncoding RNAs (lncRNAs). Since MYC is a ubiquitous oncoprotein, some of these lncRNAs probably play a significant role in cancer. We applied CRISPR interference (CRISPRi) to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 noncoding loci that play positive roles in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RT-qPCR and in CRISPRi competition assays with individual GFP-expressing sgRNA constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID (SIN3-interacting domain) derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, SID is superior to the KRAB repressor domain, which serves routinely as a transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP, allowing the construction of a doxycycline-regulatable CRISPRi system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.
Collapse
Affiliation(s)
- Philipp Raffeiner
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan R Hart
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Liron Bar-Peled
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Marc S Weinberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Peter K Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037;
| |
Collapse
|