251
|
Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
Collapse
|
252
|
Loukil A, Tormanen K, Sütterlin C. The daughter centriole controls ciliogenesis by regulating Neurl-4 localization at the centrosome. J Cell Biol 2017; 216:1287-1300. [PMID: 28385950 PMCID: PMC5412565 DOI: 10.1083/jcb.201608119] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/29/2016] [Accepted: 02/28/2017] [Indexed: 12/26/2022] Open
Abstract
During ciliogenesis, the daughter centriole is found next to the mother, but its role in this process is not known. Loukil et al. show that a daughter centriole is necessary for primary cilia formation by promoting Neurl-4–dependent removal of the negative ciliogenesis regulator CP110 from the mother. The two centrioles of the centrosome differ in age and function. Although the mother centriole mediates most centrosome-dependent processes, the role of the daughter remains poorly understood. A recent study has implicated the daughter centriole in centriole amplification in multiciliated cells, but its contribution to primary ciliogenesis is unclear. We found that manipulations that prevent daughter centriole formation or induce its separation from the mother abolish ciliogenesis. This defect was caused by stabilization of the negative ciliogenesis regulator CP110 and was corrected by CP110 depletion. CP110 dysregulation may be caused by effects on Neurl-4, a daughter centriole–associated ubiquitin ligase cofactor, which was required for ciliogenesis. Centrosome-targeted Neurl-4 was sufficient to restore ciliogenesis in cells with manipulated daughter centrioles. Interestingly, early during ciliogenesis, Neurl-4 transiently associated with the mother centriole in a process that required mother–daughter centriole proximity. Our data support a model in which the daughter centriole promotes ciliogenesis through Neurl-4–dependent regulation of CP110 levels at the mother centriole.
Collapse
Affiliation(s)
- Abdelhalim Loukil
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Kati Tormanen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Christine Sütterlin
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
| |
Collapse
|
253
|
Lin A, Giuliano CJ, Sayles NM, Sheltzer JM. CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials. eLife 2017; 6. [PMID: 28337968 PMCID: PMC5365317 DOI: 10.7554/elife.24179] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/20/2017] [Indexed: 12/14/2022] Open
Abstract
The Maternal Embryonic Leucine Zipper Kinase (MELK) has been reported to be a genetic dependency in several cancer types. MELK RNAi and small-molecule inhibitors of MELK block the proliferation of various cancer cell lines, and MELK knockdown has been described as particularly effective against the highly-aggressive basal/triple-negative subtype of breast cancer. Based on these preclinical results, the MELK inhibitor OTS167 is currently being tested as a novel chemotherapy agent in several clinical trials. Here, we report that mutagenizing MELK with CRISPR/Cas9 has no effect on the fitness of basal breast cancer cell lines or cell lines from six other cancer types. Cells that harbor null mutations in MELK exhibit wild-type doubling times, cytokinesis, and anchorage-independent growth. Furthermore, MELK-knockout lines remain sensitive to OTS167, suggesting that this drug blocks cell division through an off-target mechanism. In total, our results undermine the rationale for a series of current clinical trials and provide an experimental approach for the use of CRISPR/Cas9 in preclinical target validation that can be broadly applied. DOI:http://dx.doi.org/10.7554/eLife.24179.001 Like a person who is dependent on coffee to be productive, cancer cells are dependent on the products of certain genes in order to dominate their environment and grow. Cancer cells will stop growing and die when the activity of these gene products is blocked. These genes are known as cancer dependencies or “addictions”. As a result, researchers are constantly looking for cancer dependencies and developing drugs to block their activity. It was previously believed that a gene called MELK was an addiction in certain types of breast cancer. In fact, pharmaceutical companies had developed a drug to block the activity of MELK, and this drug is currently being tested in human patients. However, Lin, Giuliano et al. have now taken a second look at the role of MELK in breast cancer, and have come to a different conclusion. Using a gene editing technology called CRISPR/Cas9, Lin, Giuliano et al. removed MELK activity from several cancer cell lines. This did not stop cancer cells from multiplying, suggesting that MELK is not actually a cancer addiction. Additionally, when breast cancer cells that do not produce MELK were exposed to the drug that is supposed to block MELK activity, the drug still stopped cell growth. Since the drug works when MELK is not present in the cell, the drug must be binding to other proteins. This suggests that MELK is not the actual target of the drug. Lin, Giuliano et al. suggest that, in the future, CRISPR/Cas9 technology could be used to better identify cancer dependencies and drug targets before cancer drugs are given to human patients. DOI:http://dx.doi.org/10.7554/eLife.24179.002
Collapse
Affiliation(s)
- Ann Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Stony Brook University, Stony Brook, United States
| | - Christopher J Giuliano
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Stony Brook University, Stony Brook, United States
| | - Nicole M Sayles
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Jason M Sheltzer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| |
Collapse
|
254
|
Kaya H, Numa H, Nishizawa-Yokoi A, Toki S, Habu Y. DNA Methylation Affects the Efficiency of Transcription Activator-Like Effector Nucleases-Mediated Genome Editing in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:302. [PMID: 28348570 PMCID: PMC5346537 DOI: 10.3389/fpls.2017.00302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/20/2017] [Indexed: 05/28/2023]
Abstract
Genome editing in plants becomes popular since the advent of sequence-specific nucleases (SSNs) that are simple to set up and efficient in various plant species. Although transcription activator-like effector nucleases (TALENs) are one of the most prevalent SSNs and have a potential to provide higher target specificity by their dimeric property, TALENs are sensitive to methylated cytosines that are present not only in transposons but also in active genes in plants. In mammalian cells, the methylation sensitivity of TALENs could be overcome by using a base-recognition module (N∗) that has a higher affinity to methylated cytosine. In contrast to mammals, plants carry DNA methylation at all cytosine contexts (CG, CHG, and CHH, where H represents A, C, or T) with various degrees and effectiveness of N∗ module in genome editing in plants has not been explored. In this study, we designed sets of TALENs with or without N∗ modules and examined their efficiency in genome editing of methylated regions in rice. Although improvement in genome editing efficiency was observed with N∗-TALENs designed to a stably methylated target, another target carrying cytosines with various levels of methylation showed resistance to both normal and N∗-TALENs. The results suggest that variability of cytosine methylation in target regions is an additional factor affecting the genome editing efficiency of TALENs.
Collapse
Affiliation(s)
- Hidetaka Kaya
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Hisataka Numa
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Yoshiki Habu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| |
Collapse
|
255
|
Romay G, Bragard C. Antiviral Defenses in Plants through Genome Editing. Front Microbiol 2017; 8:47. [PMID: 28167937 PMCID: PMC5253358 DOI: 10.3389/fmicb.2017.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/06/2017] [Indexed: 01/29/2023] Open
Abstract
Plant-virus interactions based-studies have contributed to increase our understanding on plant resistance mechanisms, providing new tools for crop improvement. In the last two decades, RNA interference, a post-transcriptional gene silencing approach, has been used to induce antiviral defenses in plants with the help of genetic engineering technologies. More recently, the new genome editing systems (GES) are revolutionizing the scope of tools available to confer virus resistance in plants. The most explored GES are zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 endonuclease. GES are engineered to target and introduce mutations, which can be deleterious, via double-strand breaks at specific DNA sequences by the error-prone non-homologous recombination end-joining pathway. Although GES have been engineered to target DNA, recent discoveries of GES targeting ssRNA molecules, including virus genomes, pave the way for further studies programming plant defense against RNA viruses. Most of plant virus species have an RNA genome and at least 784 species have positive ssRNA. Here, we provide a summary of the latest progress in plant antiviral defenses mediated by GES. In addition, we also discuss briefly the GES perspectives in light of the rebooted debate on genetic modified organisms (GMOs) and the current regulatory frame for agricultural products involving the use of such engineering technologies.
Collapse
Affiliation(s)
- Gustavo Romay
- Applied Microbiology – Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Claude Bragard
- Applied Microbiology – Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| |
Collapse
|
256
|
Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
Collapse
|
257
|
Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 DOI: 10.3389/fpls.2017.01364/bibtex] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/20/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
Collapse
Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| |
Collapse
|
258
|
Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 PMCID: PMC5541054 DOI: 10.3389/fpls.2017.01364] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/17/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
Collapse
Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K. Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
- *Correspondence: Chunpeng Song,
| |
Collapse
|
259
|
Hansen SVF, Ulven T. Pharmacological Tool Compounds for the Free Fatty Acid Receptor 4 (FFA4/GPR120). Handb Exp Pharmacol 2017; 236:33-56. [PMID: 27807695 DOI: 10.1007/164_2016_60] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The free fatty acid receptor 4 (FFA4), also known as GPR120, is a G protein-coupled receptor that is activated by long-chain fatty acids and that has been associated with regulation of appetite, release of insulin controlling hormones, insulin sensitization, anti-inflammatory and potentially anti-obesity activity, and is progressively appearing as an attractive potential target for the treatment of metabolic dysfunctions such as obesity, type 2 diabetes and inflammatory disorders. Ongoing investigations of the pharmacological functions of FFA4 and validation of its potential as a therapeutic target depend critically on the appropriateness and quality of the available pharmacological probes or tool compounds. After a brief summary of the pharmacological functions of FFA4 and some general considerations on desirable properties for these pharmacological tool compounds, the individual compounds that have been or are currently being used as tools for probing the function of FFA4 in various in vitro and in vivo settings will be discussed and evaluated.
Collapse
Affiliation(s)
- Steffen V F Hansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| |
Collapse
|
260
|
Hough SH, Ajetunmobi A. The Future of CRISPR Applications in the Lab, the Clinic and Society. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:157-178. [PMID: 29130159 DOI: 10.1007/978-3-319-63904-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) has emerged as one of the premiere biological tools of the century. Even more so than older genome editing techniques such as TALENs and ZFNs, CRISPR provides speed and ease-of-use heretofore unheard of in agriculture, the environment and human health. The ability to map the function of virtually every component of the genome in a scalable, multiplexed manner is unprecedented. Once those regions have been explored, CRISPR also presents an opportunity to take advantage of endogenous cellular repair pathways to change and precisely edit the genome [1-3]. In the case of human health, CRISPR operates as both a tool of discovery and a solution to fundamental problems behind disease and undesirable mutations.
Collapse
Affiliation(s)
- Soren H Hough
- Department of Microbiology, University of Massachusetts Amherst, 418 Morrill Science Center IVN, 649 North Pleasant Street, Amherst, MA, 01003, USA.
| | - Ayokunmi Ajetunmobi
- Department of Clinical Medicine, St. James' Hospital, Dublin, Ireland, James's Street, Dublin 8, Dublin, Leinster, D08 NHY1, Ireland
| |
Collapse
|
261
|
Martinez E, Sanchez L, Vazquez N, Marks R, Cedillo R, Respondek C, Holguin M, Persans MW, Keniry M. A CRISPR View of Biological Mechanisms. Discoveries (Craiova) 2016; 4:e69. [PMID: 32309588 PMCID: PMC7159838 DOI: 10.15190/d.2016.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 12/26/2022] Open
Abstract
A decade ago, only six manuscripts would be found on a PubMed search for "CRISPR," compared to 2,011 manuscripts in 2016. The purpose of this review is to discuss this emergent technology that has revolutionized molecular biological research in just a few years. Endogenous CRISPR mechanisms are harbored by bacteria and archaea as an adaptive defense system that targets foreign DNA from viruses and plasmids. CRISPR has been adapted as a genome editing tool in a plethora of organisms ranging from yeast to humans. This tool has been employed to create loss of function mutations, gain of function mutations, and tagged alleles in a wide range of settings. CRISPR is now extensively employed for genetic screens. CRISPR has also been adapted to study transcriptional regulation. This versatile and relatively facile technique has, and will be, tremendously impactful in research areas such as biomedical sciences, agriculture, and the basic sciences.
Collapse
Affiliation(s)
- Eduardo Martinez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Lilia Sanchez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Neftali Vazquez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Rebecca Marks
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Raechel Cedillo
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Christa Respondek
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Martin Holguin
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Michael W. Persans
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Megan Keniry
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| |
Collapse
|
262
|
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing. Cell 2016; 167:219-232.e14. [PMID: 27662090 PMCID: PMC5039111 DOI: 10.1016/j.cell.2016.09.006] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/18/2016] [Accepted: 09/02/2016] [Indexed: 12/29/2022]
Abstract
Gene silencing is instrumental to interrogate gene function and holds promise for therapeutic applications. Here, we repurpose the endogenous retroviruses’ silencing machinery of embryonic stem cells to stably silence three highly expressed genes in somatic cells by epigenetics. This was achieved by transiently expressing combinations of engineered transcriptional repressors that bind to and synergize at the target locus to instruct repressive histone marks and de novo DNA methylation, thus ensuring long-term memory of the repressive epigenetic state. Silencing was highly specific, as shown by genome-wide analyses, sharply confined to the targeted locus without spreading to nearby genes, resistant to activation induced by cytokine stimulation, and relieved only by targeted DNA demethylation. We demonstrate the portability of this technology by multiplex gene silencing, adopting different DNA binding platforms and interrogating thousands of genomic loci in different cell types, including primary T lymphocytes. Targeted epigenome editing might have broad application in research and medicine. Repurposing the ERV silencing machinery for targeted epigenetic gene silencing Hit-and-run delivery of combinations of engineered transcriptional repressors (ETRs) Inheritable and stimulation-resistant silencing of endogenous genes by DNA methylation Portable to different cell types and DNA binding platforms and amenable to multiplexing
Collapse
|
263
|
van Diemen FR, Lebbink RJ. CRISPR/Cas9, a powerful tool to target human herpesviruses. Cell Microbiol 2016; 19. [PMID: 27860066 DOI: 10.1111/cmi.12694] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Over 90% of the adult population is infected with one or multiple herpesviruses. These viruses are characterized by their ability to establish latency, where the host is unable to clear the invader from infected cells resulting in a lifelong infection. Herpesviruses cause a wide variety of (recurrent) diseases such as cold sores, shingles, congenital defects and several malignancies. Although the productive phase of a herpesvirus infection can often be efficiently limited by nucleoside analogs, these drugs are ineffective during a latent herpesvirus infection and are therefore unable to clear herpesviruses from the human host. Advances in genome engineering using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 facilitates virus research and may hold potential to treat or cure previously incurable herpesvirus infections by directly targeting these viruses within infected cells. Here, we review recent applications of the CRISPR/Cas9 system for herpesviral research and discuss the therapeutic potential of the system to treat, or even cure, productive and latent herpesviral infections.
Collapse
Affiliation(s)
- Ferdy R van Diemen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Utrecht Cornea Research Group, Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
264
|
The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
Collapse
|
265
|
Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell 2016; 167:1867-1882.e21. [PMID: 27984733 PMCID: PMC5315571 DOI: 10.1016/j.cell.2016.11.048] [Citation(s) in RCA: 654] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/14/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.
Collapse
Affiliation(s)
- Britt Adamson
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Norman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Y Cho
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuwen Chen
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline E Villalta
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Y Hein
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan A Pak
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew N Gray
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atray Dixit
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Oren Parnas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jonathan S Weissman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
266
|
Zhou H, He M, Li J, Chen L, Huang Z, Zheng S, Zhu L, Ni E, Jiang D, Zhao B, Zhuang C. Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System. Sci Rep 2016; 6:37395. [PMID: 27874087 PMCID: PMC5118805 DOI: 10.1038/srep37395] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/27/2016] [Indexed: 12/22/2022] Open
Abstract
Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new "transgene clean" TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable "transgene clean" TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new "transgene clean" TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis.
Collapse
Affiliation(s)
- Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ming He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhifeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaoyan Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Erdong Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Dagang Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, China National Hybrid Rice R&D Center, Changsha 410125, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
267
|
Leitão AL, Costa MC, Enguita FJ. Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites. J Biotechnol 2016; 241:50-60. [PMID: 27845165 DOI: 10.1016/j.jbiotec.2016.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 11/06/2016] [Accepted: 11/10/2016] [Indexed: 12/17/2022]
Abstract
Genome engineering is a branch of modern biotechnology composed of a cohort of protocols designed to construct and modify a genotype with the main objective of giving rise to a desired phenotype. Conceptually, genome engineering is based on the so called genome editing technologies, a group of genetic techniques that allow either to delete or to insert genetic information in a particular genomic locus. Ten years ago, genome editing tools were limited to virus-driven integration and homologous DNA recombination. However, nowadays the uprising of programmable nucleases is rapidly changing this paradigm. There are two main families of modern tools for genome editing depending on the molecule that controls the specificity of the system and drives the editor machinery to its place of action. Enzymes such as Zn-finger and TALEN nucleases are protein-driven genome editors; while CRISPR system is a nucleic acid-guided editing system. Genome editing techniques are still not widely applied for the design of new compounds with pharmacological activity, but they are starting to be considered as promising tools for rational genome manipulation in biotechnology applications. In this review we will discuss the potential applications of programmable nucleases for the metabolic engineering of secondary metabolites with biological activity.
Collapse
Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Campus de Caparica, 2829-516 Caparica, Portugal; MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Campus de Caparica, 2829-516 Caparica, Portugal.
| | - Marina C Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
| |
Collapse
|
268
|
Laptenko O, Tong DR, Manfredi J, Prives C. The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein. Trends Biochem Sci 2016; 41:1022-1034. [PMID: 27669647 DOI: 10.1016/j.tibs.2016.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 01/22/2023]
Abstract
The p53 tumor suppressor is a transcription factor (TF) that exerts antitumor functions through its ability to regulate the expression of multiple genes. Within the p53 protein resides a relatively short unstructured C-terminal domain (CTD) that remarkably participates in virtually every aspect of p53 performance as a TF. Because these aspects are often interdependent and it is not always possible to dissect them experimentally, there has been a great deal of controversy about the CTD. In this review we evaluate the significance and key features of this interesting region of p53 and its impact on the many aspects of p53 function in light of previous and more recent findings.
Collapse
Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - David R Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James Manfredi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
269
|
Fuchs M, Boulanger MC, Lambert H, Landry J, Lavoie JN. Adenofection: A Method for Studying the Role of Molecular Chaperones in Cellular Morphodynamics by Depletion-Rescue Experiments. J Vis Exp 2016. [PMID: 27685647 DOI: 10.3791/54557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cellular processes such as mitosis and cell differentiation are governed by changes in cell shape that largely rely on proper remodeling of the cell cytoskeletal structures. This involves the assembly-disassembly of higher-order macromolecular structures at a given time and location, a process that is particularly sensitive to perturbations caused by overexpression of proteins. Methods that can preserve protein homeostasis and maintain near-to-normal cellular morphology are highly desirable to determine the functional contribution of a protein of interest in a wide range of cellular processes. Transient depletion-rescue experiments based on RNA interference are powerful approaches to analyze protein functions and structural requirements. However, reintroduction of the target protein with minimum deviation from its physiological level is a real challenge. Here we describe a method termed adenofection that was developed to study the role of molecular chaperones and partners in the normal operation of dividing cells and the relationship with actin remodeling. HeLa cells were depleted of BAG3 with siRNA duplexes targeting the 3'UTR region. GFP-tagged BAG3 proteins were reintroduced simultaneously into >75% of the cells using recombinant adenoviruses coupled to transfection reagents. Adenofection enabled to express BAG3-GFP proteins at near physiological levels in HeLa cells depleted of BAG3, in the absence of a stress response. No effect was observed on the levels of endogenous Heat Shock Protein chaperones, the main stress-inducible regulators of protein homeostasis. Furthermore, by adding baculoviruses driving the expression of fluorescent markers at the time of cell transduction-transfection, we could dissect mitotic cell dynamics by time-lapse microscopic analyses with minimum perturbation of normal mitotic progression. Adenofection is applicable also to hard-to-infect mouse cells, and suitable for functional analyses of myoblast differentiation into myotubes. Thus adenofection provides a versatile method to perform structure-function analyses of proteins involved in sensitive biological processes that rely on higher-order cytoskeletal dynamics.
Collapse
Affiliation(s)
- Margit Fuchs
- Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Centre de recherche sur le cancer de l'Université Laval; Oncology, Centre de recherche du CHU de Québec, Université Laval
| | - Marie-Chloé Boulanger
- Laboratoire d'études moléculaires des valvulopathies (LEMV), Groupe de recherche en valvulopathies (GRV), Quebec Heart and Lung Institute/Research Center; Department of Surgery, Université Laval
| | - Herman Lambert
- Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Centre de recherche sur le cancer de l'Université Laval; Oncology, Centre de recherche du CHU de Québec, Université Laval
| | - Jacques Landry
- Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Centre de recherche sur le cancer de l'Université Laval; Oncology, Centre de recherche du CHU de Québec, Université Laval
| | - Josée N Lavoie
- Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Centre de recherche sur le cancer de l'Université Laval; Oncology, Centre de recherche du CHU de Québec, Université Laval;
| |
Collapse
|
270
|
Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis. Biotechnol Adv 2016; 34:1046-1063. [DOI: 10.1016/j.biotechadv.2016.06.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/08/2016] [Accepted: 06/12/2016] [Indexed: 12/12/2022]
|
271
|
Lopez Sanchez M, Crowston J, Mackey D, Trounce I. Emerging Mitochondrial Therapeutic Targets in Optic Neuropathies. Pharmacol Ther 2016; 165:132-52. [DOI: 10.1016/j.pharmthera.2016.06.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 12/14/2022]
|
272
|
Mutlu N, Kumar A. Mapping paths: new approaches to dissect eukaryotic signaling circuitry. F1000Res 2016; 5. [PMID: 27540473 PMCID: PMC4965690 DOI: 10.12688/f1000research.8818.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic cells are precisely “wired” to coordinate changes in external and intracellular signals with corresponding adjustments in the output of complex and often interconnected signaling pathways. These pathways are critical in understanding cellular growth and function, and several experimental trends are emerging with applicability toward more fully describing the composition and topology of eukaryotic signaling networks. In particular, recent studies have implemented CRISPR/Cas-based screens in mouse and human cell lines for genes involved in various cell growth and disease phenotypes. Proteomic methods using mass spectrometry have enabled quantitative and dynamic profiling of protein interactions, revealing previously undiscovered complexes and allele-specific protein interactions. Methods for the single-cell study of protein localization and gene expression have been integrated with computational analyses to provide insight into cell signaling in yeast and metazoans. In this review, we present an overview of exemplary studies using the above approaches, relevant for the analysis of cell signaling and indeed, more broadly, for many modern biological applications.
Collapse
Affiliation(s)
- Nebibe Mutlu
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
273
|
Lin CL, Kao JH. Review article: novel therapies for hepatitis B virus cure - advances and perspectives. Aliment Pharmacol Ther 2016; 44:213-22. [PMID: 27302653 DOI: 10.1111/apt.13694] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/26/2016] [Accepted: 05/21/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Current anti-viral therapies, interferon and nucleos(t)ide analogues, have been proven to reduce the progression of chronic hepatitis B (CHB). However, covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) persists, resulting in viral relapse after the discontinuation of treatment. AIM To discuss and review novel therapies for chronic hepatitis B infection. METHODS Recent published studies which searched from PubMed were comprehensive reviewed. The key words include chronic hepatitis B, hepatitis B virus cure, covalently closed circular DNA, direct acting anti-virals and host targeting agents. RESULTS Several novel agents through viral and host targets approaches are under investigations towards functional cure of HBV. On the one hand, direct acting anti-virals targeting virus itself, such as HBV new polymerase inhibitor, entry inhibitor, engineered site-specific nucleases and RNA interference, could inhibit amplification of cccDNA as well as intrahepatic HBV infection and eliminate or silence cccDNA transcription. Inhibitors of HBV nucleocapsid assembly suppress capsid formation and prevent synthesis of HBV DNA. On the other hand, host targeting agents (HTA) include lymphotoxin-β receptor agonist, toll-like receptor agonist, immune checkpoint inhibitors and adenovirus-based therapeutic vaccine. Through enhancing innate and adaptive immune responses, these agents could induce noncytolytic destruction of cccDNA or attack HBV-infected hepatocytes. CONCLUSION With these promising approaches, we hope to reach global hepatitis B virus control in the middle of this century.
Collapse
Affiliation(s)
- C-L Lin
- Department of Gastroenterology, Renai branch, Taipei City Hospital, Taipei, Taiwan.,Department of Psychology, National Chengchi University, Taipei, Taiwan
| | - J-H Kao
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, National Taiwan University, National Taiwan University Hospital, Taipei, Taiwan.,Department of Medical Research, National Taiwan University, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
274
|
Yu B, Lu R, Yuan Y, Zhang T, Song S, Qi Z, Shao B, Zhu M, Mi F, Cheng Y. Efficient TALEN-mediated myostatin gene editing in goats. BMC DEVELOPMENTAL BIOLOGY 2016; 16:26. [PMID: 27461387 PMCID: PMC4962387 DOI: 10.1186/s12861-016-0126-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Background Myostatin (MSTN) encodes a negative regulator of skeletal muscle mass that might have applications for promoting muscle growth in livestock. In this study, we aimed to test whether targeted MSTN editing, mediated by transcription activator-like effector nucleases (TALENs), is a viable approach to create myostatin-modified goats (Capra hircus). Results We obtained a pair of TALENs (MTAL-2) that could recognize and cut the targeted MSTN site in the goat genome. Fibroblasts from pedigreed goats were co-transfected with MTAL-2, and 272 monoclonal cell strains were confirmed to have mono- or bi-allelic mutations in MSTN. Ten cell strains with different genotypes were used as donor cells for somatic cell nuclear transfer, which produced three cloned kids (K179/MSTN−/−, K52-2/MSTN+/−, and K52-1/MSTN+/+). Conclusions The results suggested that the MTAL-2 could disrupt MSTN efficiently in the goat genome. The mutated somatic cells could be used to produce MSTN-site mutated goats without developmental disruption. Thus, TALENs is an effective method for accurate genome editing to produce site-modified goats. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0126-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Baoli Yu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Rui Lu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Yuguo Yuan
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Ting Zhang
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Shaozheng Song
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Zhengqiang Qi
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Bin Shao
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Mengmin Zhu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Fei Mi
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Yong Cheng
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
| |
Collapse
|
275
|
Guernet A, Mungamuri SK, Cartier D, Sachidanandam R, Jayaprakash A, Adriouch S, Vezain M, Charbonnier F, Rohkin G, Coutant S, Yao S, Ainani H, Alexandre D, Tournier I, Boyer O, Aaronson SA, Anouar Y, Grumolato L. CRISPR-Barcoding for Intratumor Genetic Heterogeneity Modeling and Functional Analysis of Oncogenic Driver Mutations. Mol Cell 2016; 63:526-38. [PMID: 27453044 DOI: 10.1016/j.molcel.2016.06.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/10/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
Abstract
Intratumor genetic heterogeneity underlies the ability of tumors to evolve and adapt to different environmental conditions. Using CRISPR/Cas9 technology and specific DNA barcodes, we devised a strategy to recapitulate and trace the emergence of subpopulations of cancer cells containing a mutation of interest. We used this approach to model different mechanisms of lung cancer cell resistance to EGFR inhibitors and to assess effects of combined drug therapies. By overcoming intrinsic limitations of current approaches, CRISPR-barcoding also enables investigation of most types of genetic modifications, including repair of oncogenic driver mutations. Finally, we used highly complex barcodes inserted at a specific genome location as a means of simultaneously tracing the fates of many thousands of genetically labeled cancer cells. CRISPR-barcoding is a straightforward and highly flexible method that should greatly facilitate the functional investigation of specific mutations, in a context that closely mimics the complexity of cancer.
Collapse
Affiliation(s)
- Alexis Guernet
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Sathish Kumar Mungamuri
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dorthe Cartier
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anitha Jayaprakash
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sahil Adriouch
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Flow Cytometry and Cell Sorting Facility, 76000 Rouen, France
| | - Myriam Vezain
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Genomics Facility,76000 Rouen, France
| | - Françoise Charbonnier
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Genomics Facility,76000 Rouen, France
| | - Guy Rohkin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sophie Coutant
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Genomics Facility,76000 Rouen, France
| | - Shen Yao
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hassan Ainani
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - David Alexandre
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Isabelle Tournier
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Genomics Facility,76000 Rouen, France
| | - Olivier Boyer
- Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France; IRIB Flow Cytometry and Cell Sorting Facility, 76000 Rouen, France; Department of Immunology, CHU Rouen, 76000 Rouen, France
| | - Stuart A Aaronson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Youssef Anouar
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Luca Grumolato
- Normandie Univ, UNIROUEN, INSERM, DC2N, 76000 Rouen, France; Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France.
| |
Collapse
|
276
|
Wilson JL, Dalin S, Gosline S, Hemann M, Fraenkel E, Lauffenburger DA. Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia. Integr Biol (Camb) 2016; 8:761-74. [PMID: 27315426 PMCID: PMC5224708 DOI: 10.1039/c6ib00040a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022]
Abstract
Data integration stands to improve interpretation of RNAi screens which, as a result of off-target effects, typically yield numerous gene hits of which only a few validate. These off-target effects can result from seed matches to unintended gene targets (reagent-based) or cellular pathways, which can compensate for gene perturbations (biology-based). We focus on the biology-based effects and use network modeling tools to discover pathways de novo around RNAi hits. By looking at hits in a functional context, we can uncover novel biology not identified from any individual 'omics measurement. We leverage multiple 'omic measurements using the Simultaneous Analysis of Multiple Networks (SAMNet) computational framework to model a genome scale shRNA screen investigating Acute Lymphoblastic Leukemia (ALL) progression in vivo. Our network model is enriched for cellular processes associated with hematopoietic differentiation and homeostasis even though none of the individual 'omic sets showed this enrichment. The model identifies genes associated with the TGF-beta pathway and predicts a role in ALL progression for many genes without this functional annotation. We further experimentally validate the hidden genes - Wwp1, a ubiquitin ligase, and Hgs, a multi-vesicular body associated protein - for their role in ALL progression. Our ALL pathway model includes genes with roles in multiple types of leukemia and roles in hematological development. We identify a tumor suppressor role for Wwp1 in ALL progression. This work demonstrates that network integration approaches can compensate for off-target effects, and that these methods can uncover novel biology retroactively on existing screening data. We anticipate that this framework will be valuable to multiple functional genomic technologies - siRNA, shRNA, and CRISPR - generally, and will improve the utility of functional genomic studies.
Collapse
Affiliation(s)
- Jennifer L. Wilson
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , 16-343 , Cambridge MA 02139 , USA . ; ; Tel: +1-617-252-1629
| | - Simona Dalin
- Department of Biology , Massachusetts Institute of Technology , Cambridge MA 02139 , USA
| | - Sara Gosline
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , 16-343 , Cambridge MA 02139 , USA . ; ; Tel: +1-617-252-1629
| | - Michael Hemann
- Department of Biology , Massachusetts Institute of Technology , Cambridge MA 02139 , USA
| | - Ernest Fraenkel
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , 16-343 , Cambridge MA 02139 , USA . ; ; Tel: +1-617-252-1629
- Department of Biology , Massachusetts Institute of Technology , Cambridge MA 02139 , USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , 16-343 , Cambridge MA 02139 , USA . ; ; Tel: +1-617-252-1629
| |
Collapse
|
277
|
CRISPR-Cas9 technology: applications and human disease modelling. Brief Funct Genomics 2016; 16:4-12. [DOI: 10.1093/bfgp/elw025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
278
|
Zhu Z, Ihle NT, Rejto PA, Zarrinkar PP. Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine. BMC Genomics 2016; 17:455. [PMID: 27296290 PMCID: PMC4907009 DOI: 10.1186/s12864-016-2807-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 05/27/2016] [Indexed: 01/22/2023] Open
Abstract
Background Genome-scale functional genomic screens across large cell line panels provide a rich resource for discovering tumor vulnerabilities that can lead to the next generation of targeted therapies. Their data analysis typically has focused on identifying genes whose knockdown enhances response in various pre-defined genetic contexts, which are limited by biological complexities as well as the incompleteness of our knowledge. We thus introduce a complementary data mining strategy to identify genes with exceptional sensitivity in subsets, or outlier groups, of cell lines, allowing an unbiased analysis without any a priori assumption about the underlying biology of dependency. Results Genes with outlier features are strongly and specifically enriched with those known to be associated with cancer and relevant biological processes, despite no a priori knowledge being used to drive the analysis. Identification of exceptional responders (outliers) may not lead only to new candidates for therapeutic intervention, but also tumor indications and response biomarkers for companion precision medicine strategies. Several tumor suppressors have an outlier sensitivity pattern, supporting and generalizing the notion that tumor suppressors can play context-dependent oncogenic roles. Conclusions The novel application of outlier analysis described here demonstrates a systematic and data-driven analytical strategy to decipher large-scale functional genomic data for oncology target and precision medicine discoveries. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2807-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhou Zhu
- Oncology Research Unit, Pfizer Worldwide Research & Development, La Jolla Laboratories, 10777 Science Center Drive, San Diego, CA, 92121, USA.
| | - Nathan T Ihle
- Oncology Research Unit, Pfizer Worldwide Research & Development, La Jolla Laboratories, 10777 Science Center Drive, San Diego, CA, 92121, USA
| | - Paul A Rejto
- Oncology Research Unit, Pfizer Worldwide Research & Development, La Jolla Laboratories, 10777 Science Center Drive, San Diego, CA, 92121, USA
| | - Patrick P Zarrinkar
- Oncology Research Unit, Pfizer Worldwide Research & Development, La Jolla Laboratories, 10777 Science Center Drive, San Diego, CA, 92121, USA.
| |
Collapse
|
279
|
Wang F, Zhang H, Gao J, Chen F, Chen S, Zhang C, Peng G. Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides. Biotechniques 2016; 60:299-305. [PMID: 27286807 DOI: 10.2144/000114422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/08/2016] [Indexed: 11/23/2022] Open
Abstract
Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.
Collapse
Affiliation(s)
- Fenghua Wang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Hefei Zhang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Jingxia Gao
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Fengjiao Chen
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Sijie Chen
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Cuizhen Zhang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Gang Peng
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| |
Collapse
|
280
|
Mao XY, Dai JX, Zhou HH, Liu ZQ, Jin WL. Brain tumor modeling using the CRISPR/Cas9 system: state of the art and view to the future. Oncotarget 2016; 7:33461-71. [PMID: 26993776 PMCID: PMC5078110 DOI: 10.18632/oncotarget.8075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/29/2016] [Indexed: 12/26/2022] Open
Abstract
Although brain tumors have been known tremendously over the past decade, there are still many problems to be solved. The etiology of brain tumors is not well understood and the treatment remains modest. There is in great need to develop a suitable brain tumor models that faithfully mirror the etiology of human brain neoplasm and subsequently get more efficient therapeutic approaches for these disorders. In this review, we described the current status of animal models of brain tumors and analyzed their advantages and disadvantages. Additionally, prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), a versatile genome editing technology for investigating the functions of target genes, and its application were also introduced in our present work. We firstly proposed that brain tumor modeling could be well established via CRISPR/Cas9 techniques. And CRISPR/Cas9-mediated brain tumor modeling was likely to be more suitable for figuring out the pathogenesis of brain tumors, as CRISPR/Cas9 platform was a simple and more efficient biological toolbox for implementing mutagenesis of oncogenes or tumor suppressors that were closely linked with brain tumors.
Collapse
Affiliation(s)
- Xiao-Yuan Mao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Jin-Xiang Dai
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Wei-Lin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, P. R. China
| |
Collapse
|
281
|
Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
Collapse
Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
| |
Collapse
|
282
|
Rutenberg-Schoenberg M, Sexton AN, Simon MD. The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genomics Hum Genet 2016; 17:69-94. [PMID: 27147088 DOI: 10.1146/annurev-genom-090314-024939] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs). Although little is known about the biochemical mechanisms of these lncRNAs, there is a developing consensus regarding the challenges of defining lncRNA function and mechanism. In this review, we examine the definition, discovery, functions, and mechanisms of lncRNAs. We emphasize areas where challenges remain and where consensus among laboratories has underscored the exciting ways in which human lncRNAs may affect chromatin biology.
Collapse
Affiliation(s)
- Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| |
Collapse
|
283
|
Skirycz A, Kierszniowska S, Méret M, Willmitzer L, Tzotzos G. Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado? Trends Biotechnol 2016; 34:781-790. [PMID: 27113632 DOI: 10.1016/j.tibtech.2016.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/25/2022]
Abstract
Ignorant of the New World, Europeans believed in El Dorado, a hidden city of immense wealth in gold. Many consider the Amazonian forest to be a medicinal treasure chest and potentially the largest drug dispensary in the world. Yet, the quest to obtain drugs from indigenous tropical plants remains elusive. Here, we assess the potential of new technologies to tap into the metabolic diversity of tropical plants. We also consider how regulations affect access to plant resources. We conclude that, although the road to this medicinal El Dorado may be long and arduous, many other smaller but still valuable finds are hidden along the way.
Collapse
Affiliation(s)
- Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil.
| | | | | | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - George Tzotzos
- Department of Agriculture, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil
| |
Collapse
|
284
|
Gerlai R. Gene Targeting Using Homologous Recombination in Embryonic Stem Cells: The Future for Behavior Genetics? Front Genet 2016; 7:43. [PMID: 27148349 PMCID: PMC4826881 DOI: 10.3389/fgene.2016.00043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/14/2016] [Indexed: 12/27/2022] Open
Abstract
Gene targeting with homologous recombination in embryonic stem cells created a revolution in the analysis of the function of genes in behavioral brain research. The technology allowed unprecedented precision with which one could manipulate genes and study the effect of this manipulation on the central nervous system. With gene targeting, the uncertainty inherent in psychopharmacology regarding whether a particular compound would act only through a specific target was removed. Thus, gene targeting became highly popular. However, with this popularity came the realization that like other methods, gene targeting also suffered from some technical and principal problems. For example, two decades ago, issues about compensatory changes and about genetic linkage were raised. Since then, the technology developed, and its utility has been better delineated. This review will discuss the pros and cons of the technique along with these advancements from the perspective of the neuroscientist user. It will also compare and contrast methods that may represent novel alternatives to the homologous recombination based gene targeting approach, including the TALEN and the CRISPR/Cas9 systems. The goal of the review is not to provide detailed recipes, but to attempt to present a short summary of these approaches a behavioral geneticist or neuroscientist may consider for the analysis of brain function and behavior.
Collapse
Affiliation(s)
- Robert Gerlai
- Department of Cell & Systems Biology and Department of Psychology, University of Toronto MississaugaMississauga, ON, Canada
| |
Collapse
|
285
|
TALENs-directed knockout of the full-length transcription factor Nrf1α that represses malignant behaviour of human hepatocellular carcinoma (HepG2) cells. Sci Rep 2016; 6:23775. [PMID: 27065079 PMCID: PMC4827396 DOI: 10.1038/srep23775] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
The full-length Nrf1α is processed into distinct isoforms, which together regulate genes essential for maintaining cellular homeostasis and organ integrity, and liver-specific loss of Nrf1 in mice results in spontaneous hepatoma. Herein, we report that the human constitutive Nrf1α, rather than smaller Nrf1β/γ, expression is attenuated or abolished in the case of low-differentiated high-metastatic hepatocellular carcinomas. Therefore, Nrf1α is of importance in the physio-pathological origin and development, but its specific pathobiological function(s) remains elusive. To address this, TALENs-directed knockout of Nrf1α, but not Nrf1β/γ, is created in the human hepatocellular carcinoma (HepG2) cells. The resulting Nrf1α−/− cells are elongated, with slender spindle-shapes and enlarged gaps between cells observed under scanning electron microscope. When compared with wild-type controls, the invasive and migratory abilities of Nrf1α−/− cells are increased significantly, along with the cell-cycle G2-M arrest and S-phase reduction, as accompanied by suppressed apoptosis. Despite a modest increase in the soft-agar colony formation of Nrf1α−/− cells, its loss-of-function markedly promotes malgrowth of the subcutaneous carcinoma xenograft in nude mice with hepatic metastasis. Together with molecular expression results, we thus suppose requirement of Nrf1α (and major derivates) for gene regulatory mechanisms repressing cancer cell process (e.g. EMT) and malignant behaviour (e.g. migration).
Collapse
|
286
|
Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR. CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell 2016; 18:541-53. [PMID: 26971820 DOI: 10.1016/j.stem.2016.01.022] [Citation(s) in RCA: 328] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/21/2015] [Accepted: 01/24/2016] [Indexed: 12/20/2022]
Abstract
Developing technologies for efficient and scalable disruption of gene expression will provide powerful tools for studying gene function, developmental pathways, and disease mechanisms. Here, we develop clustered regularly interspaced short palindromic repeat interference (CRISPRi) to repress gene expression in human induced pluripotent stem cells (iPSCs). CRISPRi, in which a doxycycline-inducible deactivated Cas9 is fused to a KRAB repression domain, can specifically and reversibly inhibit gene expression in iPSCs and iPSC-derived cardiac progenitors, cardiomyocytes, and T lymphocytes. This gene repression system is tunable and has the potential to silence single alleles. Compared with CRISPR nuclease (CRISPRn), CRISPRi gene repression is more efficient and homogenous across cell populations. The CRISPRi system in iPSCs provides a powerful platform to perform genome-scale screens in a wide range of iPSC-derived cell types, dissect developmental pathways, and model disease.
Collapse
Affiliation(s)
- Mohammad A Mandegar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
| | - Nathaniel Huebsch
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ekaterina B Frolov
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Edward Shin
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Annie Truong
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Michael P Olvera
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Amanda H Chan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Yuichiro Miyaoka
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Kristin Holmes
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - C Ian Spencer
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Luke M Judge
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David E Gordon
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
| | - Tilde V Eskildsen
- Department of Cardiovascular and Renal Research, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
| | - Søren P Sheikh
- Department of Cardiovascular and Renal Research, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Po-Lin So
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Bruce R Conklin
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
287
|
Nastiuk KL, Krolewski JJ. Opportunities and challenges in combination gene cancer therapy. Adv Drug Deliv Rev 2016; 98:35-40. [PMID: 26724249 PMCID: PMC4957561 DOI: 10.1016/j.addr.2015.12.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/28/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023]
Abstract
Treatment for solid tumor malignancies, which constitute the majority of human cancers, is still dominated by surgery and radiotherapies. This is especially true for many localized solid tumors, which are often curable with these treatments. However, metastatic cancers are beyond the reach of these therapies, and many localized cancers that are initially treated with surgery and radiation will recur and metastasize. Thus, for over 60years there has been a concerted effort to develop effective drug treatments for metastatic cancers. Combination therapies are an increasingly important part of the anti-cancer drug armamentarium. In the case of cytotoxic chemotherapy, multi-drug regimens rapidly became the norm, as the earliest single agents were relatively ineffective. In contrast to chemotherapy, where combination therapies were required in order to achieve treatment efficacy, for both hormonal and targeted therapies the impetus to move toward the use of combination therapies is to prevent or reverse the development of treatment resistance. In addition, emerging evidence suggests that combination therapy may also improve cancer treatment by neutralizing an emerging treatment side effect termed therapy-induced metastasis, which accompanies some effective single agent therapies. Finally, although gene therapy is still far from use in the clinic, we propose that combination therapies may enhance its effectiveness.
Collapse
Affiliation(s)
- Kent L Nastiuk
- Department of Cancer Genetics, Elm & Carlton Streets, Buffalo, NY 14263, United States
| | - John J Krolewski
- Roswell Park Cancer Institute, Center for Personalized Medicine, United States; Department of Cancer Genetics, Elm & Carlton Streets, Buffalo, NY 14263, United States.
| |
Collapse
|
288
|
Yang B, Fujii T, Ishikawa Y, Matsuo T. Targeted mutagenesis of an odorant receptor co-receptor using TALEN in Ostrinia furnacalis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 70:53-59. [PMID: 26689645 DOI: 10.1016/j.ibmb.2015.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/30/2015] [Accepted: 12/09/2015] [Indexed: 06/05/2023]
Abstract
Genome editing using transcription activator-like effector nuclease (TALEN) has been applied for various model organisms but not yet for agricultural pest insects. In this study, TALEN-mediated mutagenesis of the gene encoding odorant receptor co-receptor (Orco) of an important agricultural pest Ostrinia furnacalis (OfurOrco) was carried out. Of the two pairs of TALEN constructs designed, one generated somatic and germline mutations at rates of 70.8% and 20.8%, respectively. Physiological and behavioral analyses using a gas chromatograph-electroantennographic detector system and a wind tunnel, respectively, revealed that antennal responses to sex pheromone components were decreased to trace levels, and behavioral responses were abolished in OfurOrco mutants. This study demonstrated that TALEN-mediated mutagenesis is applicable to pest insects, and these results will open the way for a better understanding of chemosensory systems in wild insects.
Collapse
Affiliation(s)
- Bin Yang
- Department of Agricultural and Environmental Biology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takeshi Fujii
- Department of Agricultural and Environmental Biology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukio Ishikawa
- Department of Agricultural and Environmental Biology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Matsuo
- Department of Agricultural and Environmental Biology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| |
Collapse
|
289
|
Unniyampurath U, Pilankatta R, Krishnan MN. RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi? Int J Mol Sci 2016; 17:291. [PMID: 26927085 PMCID: PMC4813155 DOI: 10.3390/ijms17030291] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
The recent emergence of multiple technologies for modifying gene structure has revolutionized mammalian biomedical research and enhanced the promises of gene therapy. Over the past decade, RNA interference (RNAi) based technologies widely dominated various research applications involving experimental modulation of gene expression at the post-transcriptional level. Recently, a new gene editing technology, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system, has received unprecedented acceptance in the scientific community for a variety of genetic applications. Unlike RNAi, the CRISPR/Cas9 system is bestowed with the ability to introduce heritable precision insertions and deletions in the eukaryotic genome. The combination of popularity and superior capabilities of CRISPR/Cas9 system raises the possibility that this technology may occupy the roles currently served by RNAi and may even make RNAi obsolete. We performed a comparative analysis of the technical aspects and applications of the CRISPR/Cas9 system and RNAi in mammalian systems, with the purpose of charting out a predictive picture on whether the CRISPR/Cas9 system will eclipse the existence and future of RNAi. The conclusion drawn from this analysis is that RNAi will still occupy specific domains of biomedical research and clinical applications, under the current state of development of these technologies. However, further improvements in CRISPR/Cas9 based technology may ultimately enable it to dominate RNAi in the long term.
Collapse
Affiliation(s)
- Unnikrishnan Unniyampurath
- Program on Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
| | - Rajendra Pilankatta
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Central University of Kerala, Nileshwar 671328, India.
| | - Manoj N Krishnan
- Program on Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
| |
Collapse
|
290
|
Way SW, Popko B. Harnessing the integrated stress response for the treatment of multiple sclerosis. Lancet Neurol 2016; 15:434-43. [PMID: 26873788 PMCID: PMC4792730 DOI: 10.1016/s1474-4422(15)00381-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 11/09/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022]
Abstract
Multiple sclerosis (MS) is a chronic demyelinating autoimmune disease of the central nervous system (CNS) with no known cure. Though a dozen immunomodulatory therapies exist, their impact on progression of disease appears limited. The field has hence focused on alternate strategies for treatment such as enhancing remyelination and CNS repair. Recent progress has been made on a third complimentary treatment approach that involves protecting oligodendrocytes, and the myelin they generate and maintain, from inflammatory-mediated death via enhancement of the integrated stress response (ISR). Studies in cells and mouse models of MS have demonstrated that the ISR, an innate protective pathway that maintains proteostasis, may be effectively harnessed to aid in the protection of oligodendrocytes and myelin during inflammation. With one ISR-modifying drug already in clinical trial and a number of potential future therapies under investigation, this approach may offer an important component in halting the progression of multiple sclerosis.
Collapse
Affiliation(s)
- Sharon W Way
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, Chicago, IL, USA
| | - Brian Popko
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
291
|
A CRISPR-Based Toolbox for Studying T Cell Signal Transduction. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5052369. [PMID: 27057542 PMCID: PMC4753324 DOI: 10.1155/2016/5052369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 11/21/2022]
Abstract
CRISPR/Cas9 system is a powerful technology to perform genome editing in a variety of cell types. To facilitate the application of Cas9 in mapping T cell signaling pathways, we generated a toolbox for large-scale genetic screens in human Jurkat T cells. The toolbox has three different Jurkat cell lines expressing distinct Cas9 variants, including wild-type Cas9, dCas9-KRAB, and sunCas9. We demonstrated that the toolbox allows us to rapidly disrupt endogenous gene expression at the DNA level and to efficiently repress or activate gene expression at the transcriptional level. The toolbox, in combination with multiple currently existing genome-wide sgRNA libraries, will be useful to systematically investigate T cell signal transduction using both loss-of-function and gain-of-function genetic screens.
Collapse
|
292
|
The Rise of CRISPR/Cas for Genome Editing in Stem Cells. Stem Cells Int 2016; 2016:8140168. [PMID: 26880991 PMCID: PMC4736575 DOI: 10.1155/2016/8140168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 12/26/2022] Open
Abstract
Genetic manipulation is a powerful tool to establish the causal relationship between a genetic lesion and a particular pathological phenotype. The rise of CRISPR/Cas9 genome-engineering tools overcame the traditional technical bottleneck for routine site-specific genetic manipulation in cells. To create the perfect in vitro cell model, there is significant interest from the stem cell research community to adopt this fast evolving technology. This review addresses this need directly by providing both the up-to-date biochemical rationale of CRISPR-mediated genome engineering and detailed practical guidelines for the design and execution of CRISPR experiments in cell models. Ultimately, this review will serve as a timely and comprehensive guide for this fast developing technology.
Collapse
|
293
|
Methods to Study Long Noncoding RNA Biology in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:69-107. [PMID: 27376732 DOI: 10.1007/978-981-10-1498-7_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been discovered in recent years. The functions of lncRNAs range broadly from regulating chromatin structure and gene expression in the nucleus to controlling messenger RNA (mRNA) processing, mRNA posttranscriptional regulation, cellular signaling, and protein activity in the cytoplasm. Experimental and computational techniques have been developed to characterize lncRNAs in high-throughput scale, to study the lncRNA function in vitro and in vivo, to map lncRNA binding sites on the genome, and to capture lncRNA-protein interactions with the identification of lncRNA-binding partners, binding sites, and interaction determinants. In this chapter, we will discuss these technologies and their applications in decoding the functions of lncRNAs. Understanding these techniques including their advantages and disadvantages and developing them in the future will be essential to elaborate the roles of lncRNAs in cancer and other diseases.
Collapse
|
294
|
Abstract
Neuroscience research has been revolutionized by the use of recombinant viral vector technology from the basic, preclinical and clinical levels. Currently, multiple recombinant viral vector types are employed with each having its strengths and weaknesses depending on the proposed application. Helper-dependent adenoviral vectors (HdAd) are emerging as ideal viral vectors that solve a major need in the neuroscience field: (1) expression of transgenes that are too large to be packaged by other viral vectors and (2) rapid onset of transgene expression in the absence of cytotoxicity. Here, we describe the methods for large-scale production of HdAd viral vectors for in vivo use with neurospecific transgene expression.
Collapse
|
295
|
Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
Collapse
Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| |
Collapse
|
296
|
Vandemoortele G, Gevaert K, Eyckerman S. Proteomics in the genome engineering era. Proteomics 2015; 16:177-87. [DOI: 10.1002/pmic.201500262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Giel Vandemoortele
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| |
Collapse
|
297
|
Patel VB, McLean BA, Chen X, Oudit GY. Regulators of G-Protein Signaling 10 and Heart Failure: The Importance of Negative Regulators of Heart Disease. Hypertension 2015; 67:38-40. [PMID: 26573716 DOI: 10.1161/hypertensionaha.115.06109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Vaibhav B Patel
- From the Division of Cardiology, Department of Medicine (V.B.P., X.C., G.Y.O.), Mazankowski Alberta Heart Institute (V.B.P., B.A.M., X.C., G.Y.O.), and Department of Physiology (B.A.M., G.Y.O.), University of Alberta, Edmonton, Alberta, Canada
| | - Brent A McLean
- From the Division of Cardiology, Department of Medicine (V.B.P., X.C., G.Y.O.), Mazankowski Alberta Heart Institute (V.B.P., B.A.M., X.C., G.Y.O.), and Department of Physiology (B.A.M., G.Y.O.), University of Alberta, Edmonton, Alberta, Canada
| | - Xueyi Chen
- From the Division of Cardiology, Department of Medicine (V.B.P., X.C., G.Y.O.), Mazankowski Alberta Heart Institute (V.B.P., B.A.M., X.C., G.Y.O.), and Department of Physiology (B.A.M., G.Y.O.), University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- From the Division of Cardiology, Department of Medicine (V.B.P., X.C., G.Y.O.), Mazankowski Alberta Heart Institute (V.B.P., B.A.M., X.C., G.Y.O.), and Department of Physiology (B.A.M., G.Y.O.), University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
298
|
Belikov AV, Schraven B, Simeoni L. T cells and reactive oxygen species. J Biomed Sci 2015; 22:85. [PMID: 26471060 PMCID: PMC4608155 DOI: 10.1186/s12929-015-0194-3] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) have been long considered simply as harmful by-products of metabolism, which damage cellular proteins, lipids, and nucleic acids. ROS are also known as a weapon of phagocytes, employed against pathogens invading the host. However, during the last decade, an understanding has emerged that ROS also have important roles as signaling messengers in a multitude of pathways, in all cells, tissues, and organs. T lymphocytes are the key players of the adaptive immune response, which both coordinate other immune cells and destroy malignant and virus-infected cells. ROS have been extensively implicated in T-cell hyporesponsiveness, apoptosis, and activation. It has also become evident that the source, the kinetics, and the localization of ROS production all influence cell responses. Thus, the characterization of the precise mechanisms by which ROS are involved in the regulation of T-cell functions is important for our understanding of the immune response and for the development of new therapeutic treatments against immune-mediated diseases. This review summarizes the 30-year-long history of research on ROS in T lymphocytes, with the emphasis on the physiological roles of ROS.
Collapse
Affiliation(s)
- Aleksey V Belikov
- Otto-von-Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany.
| | - Burkhart Schraven
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Leipziger Str. 44, Magdeburg, 39120, Germany.
| | - Luca Simeoni
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Leipziger Str. 44, Magdeburg, 39120, Germany.
| |
Collapse
|
299
|
Shen S, Xia JX, Wang J. Nanomedicine-mediated cancer stem cell therapy. Biomaterials 2015; 74:1-18. [PMID: 26433488 DOI: 10.1016/j.biomaterials.2015.09.037] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 12/19/2022]
Abstract
Circumstantial evidence suggests that most tumours are heterogeneous and contain a small population of cancer stem cells (CSCs) that exhibit distinctive self-renewal, proliferation and differentiation capabilities, which are believed to play a crucial role in tumour progression, drug resistance, recurrence and metastasis in multiple malignancies. Given that the existence of CSCs is a primary obstacle to cancer therapy, a tremendous amount of effort has been put into the development of anti-CSC strategies, and several potential approaches to kill therapeutically-resistant CSCs have been explored, including inhibiting ATP-binding cassette transporters, blocking essential signalling pathways involved in self-renewal and survival of CSCs, targeting CSCs surface markers and destroying the tumour microenvironment. Meanwhile, an increasing number of therapeutic agents (e.g. small molecule drugs, nucleic acids and antibodies) to selectively target CSCs have been screened or proposed in recent years. Drug delivery technology-based approaches hold great potential for tackling the limitations impeding clinical applications of CSC-specific agents, such as poor water solubility, short circulation time and inconsistent stability. Properly designed nanocarrier-based therapeutic agents (or nanomedicines) offer new possibilities of penetrating CSC niches and significantly increasing therapeutic drug accumulation in CSCs, which are difficult for free drug counterparts. In addition, intelligent nanomedicine holds great promise to overcome pump-mediated multidrug resistance which is driven by ATP and to decrease detrimental effects on normal somatic stem cells. In this review, we summarise the distinctive biological processes related to CSCs to highlight strategies against inherently drug-resistant CSCs. We then focus on some representative examples that give a glimpse into state-of-the-art nanomedicine approaches developed for CSCs elimination. A perspective on innovative therapeutic strategies and the potential direction of nanomedicine-based CSC therapy in the near future is also presented.
Collapse
Affiliation(s)
- Song Shen
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui 230027, PR China
| | - Jin-Xing Xia
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui 230027, PR China.
| | - Jun Wang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230027, PR China; High Magnetic Field Laboratory of CAS, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
| |
Collapse
|
300
|
Decoding protein networks during virus entry by quantitative proteomics. Virus Res 2015; 218:25-39. [PMID: 26365680 PMCID: PMC4914609 DOI: 10.1016/j.virusres.2015.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/31/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023]
Abstract
Virus entry into host cells relies on interactions between viral and host structures including lipids, carbohydrates and proteins. Particularly, protein–protein interactions between viral surface proteins and host proteins as well as secondary host protein–protein interactions play a pivotal role in coordinating virus binding and uptake. These interactions are dynamic and frequently involve multiprotein complexes. In the past decade mass spectrometry based proteomics methods have reached sensitivities and high throughput compatibilities of genomics methods and now allow the reliable quantitation of proteins in complex samples from limited material. As proteomics provides essential information on the biologically active entity namely the protein, including its posttranslational modifications and its interactions with other proteins, it is an indispensable method in the virologist's toolbox. Here we review protein interactions during virus entry and compare classical biochemical methods to study entry with novel technically advanced quantitative proteomics techniques. We highlight the value of quantitative proteomics in mapping functional virus entry networks, discuss the benefits and limitations and illustrate how the methodology will help resolve unsettled questions in virus entry research in the future.
Collapse
|