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Abstract
Genomic DNA sequencing technologies have been one of the great advances of the 21st century, having decreased in cost by seven orders of magnitude and opening up new fields of investigation throughout research and clinical medicine. Genomics coupled with biochemical investigation has allowed the molecular definition of a growing number of new genetic diseases that reveal new concepts of immune regulation. Also, defining the genetic pathogenesis of these diseases has led to improved diagnosis, prognosis, genetic counseling, and, most importantly, new therapies. We highlight the investigational journey from patient phenotype to treatment using the newly defined XMEN disease, caused by the genetic loss of the MAGT1 magnesium transporter, as an example. This disease illustrates how genomics yields new fundamental immunoregulatory insights as well as how research genomics is integrated into clinical immunology. At the end, we discuss two other recently described diseases, CHAI/LATAIE (CTLA-4 deficiency) and PASLI (PI3K dysregulation), as additional examples of the journey from unknown immunological diseases to new precision medicine treatments using genomics.
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Affiliation(s)
- Michael Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
| | - Bernice Lo
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
| | - Carrie L Lucas
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
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202
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Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 2015; 17:5-15. [PMID: 26670017 DOI: 10.1038/nrm.2015.2] [Citation(s) in RCA: 569] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterial CRISPR-Cas9 system has emerged as a multifunctional platform for sequence-specific regulation of gene expression. This Review describes the development of technologies based on nuclease-deactivated Cas9, termed dCas9, for RNA-guided genomic transcription regulation, both by repression through CRISPR interference (CRISPRi) and by activation through CRISPR activation (CRISPRa). We highlight different uses in diverse organisms, including bacterial and eukaryotic cells, and summarize current applications of harnessing CRISPR-dCas9 for multiplexed, inducible gene regulation, genome-wide screens and cell fate engineering. We also provide a perspective on future developments of the technology and its applications in biomedical research and clinical studies.
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203
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Xue HY, Ji LJ, Gao AM, Liu P, He JD, Lu XJ. CRISPR-Cas9 for medical genetic screens: applications and future perspectives. J Med Genet 2015; 53:91-7. [DOI: 10.1136/jmedgenet-2015-103409] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/13/2015] [Indexed: 12/26/2022]
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204
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Hamblett KJ, Jacob AP, Gurgel JL, Tometsko ME, Rock BM, Patel SK, Milburn RR, Siu S, Ragan SP, Rock DA, Borths CJ, O'Neill JW, Chang WS, Weidner MF, Bio MM, Quon KC, Fanslow WC. SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm. Cancer Res 2015; 75:5329-40. [PMID: 26631267 DOI: 10.1158/0008-5472.can-15-1610] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/17/2015] [Indexed: 11/16/2022]
Abstract
Antibody-drug conjugates (ADC) target cytotoxic drugs to antigen-positive cells for treating cancer. After internalization, ADCs with noncleavable linkers are catabolized to amino acid-linker-warheads within the lysosome, which then enter the cytoplasm by an unknown mechanism. We hypothesized that a lysosomal transporter was responsible for delivering noncleavable ADC catabolites into the cytoplasm. To identify candidate transporters, we performed a phenotypic shRNA screen with an anti-CD70 maytansine-based ADC. This screen revealed the lysosomal membrane protein SLC46A3, the genetic attenuation of which inhibited the potency of multiple noncleavable antibody-maytansine ADCs, including ado-trastuzumab emtansine. In contrast, the potencies of noncleavable ADCs carrying the structurally distinct monomethyl auristatin F were unaffected by SLC46A3 attenuation. Structure-activity experiments suggested that maytansine is a substrate for SLC46A3. Notably, SLC46A3 silencing led to relative increases in catabolite concentrations in the lysosome. Taken together, our results establish SLC46A3 as a direct transporter of maytansine-based catabolites from the lysosome to the cytoplasm, prompting further investigation of SLC46A3 as a predictive response marker in breast cancer specimens.
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Affiliation(s)
| | - Allison P Jacob
- Amgen Inc., Therapeutic Innovation Unit, Seattle, Washington
| | - Jesse L Gurgel
- Amgen Inc., Therapeutic Innovation Unit, Seattle, Washington
| | - Mark E Tometsko
- Amgen Inc., Therapeutic Innovation Unit, Seattle, Washington
| | - Brooke M Rock
- Amgen Inc., Pharmacokinetics and Drug Metabolism, Seattle, Washington
| | - Sonal K Patel
- Amgen Inc., Pharmacokinetics and Drug Metabolism, Seattle, Washington
| | - Robert R Milburn
- Amgen Inc., Small Molecule Purification and Process Development, Thousand Oaks, California
| | - Sophia Siu
- Amgen Inc., Therapeutic Discovery, Seattle, Washington
| | | | - Dan A Rock
- Amgen Inc., Pharmacokinetics and Drug Metabolism, Seattle, Washington
| | - Christopher J Borths
- Amgen Inc., Small Molecule Purification and Process Development, Thousand Oaks, California
| | | | - Wesley S Chang
- Amgen Inc., Clinical Immunology, South San Francisco, California
| | | | - Matthew M Bio
- Amgen Inc., Small Molecule Purification and Process Development, Thousand Oaks, California
| | - Kim C Quon
- Amgen Inc., Therapeutic Innovation Unit, Seattle, Washington
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205
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Regulatory RNA-assisted genome engineering in microorganisms. Curr Opin Biotechnol 2015; 36:85-90. [DOI: 10.1016/j.copbio.2015.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/18/2015] [Accepted: 08/09/2015] [Indexed: 01/05/2023]
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206
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Kanoh H, Tong LL, Kuraishi T, Suda Y, Momiuchi Y, Shishido F, Kurata S. Genome-wide RNAi screening implicates the E3 ubiquitin ligase Sherpa in mediating innate immune signaling by Toll inDrosophilaadults. Sci Signal 2015; 8:ra107. [DOI: 10.1126/scisignal.2005971] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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207
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Nodes-and-connections RNAi knockdown screening: identification of a signaling molecule network involved in fulvestrant action and breast cancer prognosis. Oncogenesis 2015; 4:e172. [PMID: 26479444 PMCID: PMC4632093 DOI: 10.1038/oncsis.2015.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
Although RNA interference (RNAi) knockdown screening of cancer cell cultures is an effective approach to predict drug targets or therapeutic/prognostic biomarkers, interactions among identified targets often remain obscure. Here, we introduce the nodes-and-connections RNAi knockdown screening that generates a map of target interactions through systematic iterations of in silico prediction of targets and their experimental validation. An initial RNAi knockdown screening of MCF-7 human breast cancer cells targeting 6560 proteins identified four signaling molecules required for their fulvestrant-induced apoptosis. Signaling molecules physically or functionally interacting with these four primary node targets were computationally predicted and experimentally validated, resulting in identification of four second-generation nodes. Three rounds of further iterations of the prediction–validation cycle generated third, fourth and fifth generation of nodes, completing a 19-node interaction map that contained three predicted nodes but without experimental validation because of technical limitations. The interaction map involved all three members of the death-associated protein kinases (DAPKs) as well as their upstream and downstream signaling molecules (calmodulins and myosin light chain kinases), suggesting that DAPKs play critical roles in the cytocidal action of fulvestrant. The in silico Kaplan–Meier analysis of previously reported human breast cancer cohorts demonstrated significant prognostic predictive power for five of the experimentally validated nodes and for three of the prediction-only nodes. Immunohistochemical studies on the expression of 10 nodal proteins in human breast cancer tissues not only supported their prognostic prediction power but also provided statistically significant evidence of their synchronized expression, implying functional interactions among these nodal proteins. Thus, the Nodes-and-Connections approach to RNAi knockdown screening yields biologically meaningful outcomes by taking advantage of the existing knowledge of the physical and functional interactions between the predicted target genes. The resulting interaction maps provide useful information on signaling pathways cooperatively involved in clinically important features of the malignant cells, such as drug resistance.
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208
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Agrotis A, Ketteler R. A new age in functional genomics using CRISPR/Cas9 in arrayed library screening. Front Genet 2015; 6:300. [PMID: 26442115 PMCID: PMC4585242 DOI: 10.3389/fgene.2015.00300] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/10/2015] [Indexed: 12/18/2022] Open
Abstract
CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. What makes CRISPR/Cas9 so revolutionary is the ability to target a protein (Cas9) to an exact genomic locus, through designing a specific short complementary nucleotide sequence, that together with a common scaffold sequence, constitute the guide RNA bridging the protein and the DNA. Wild-type Cas9 cleaves both DNA strands at its target sequence, but this protein can also be modified to exert many other functions. For instance, by attaching an activation domain to catalytically inactive Cas9 and targeting a promoter region, it is possible to stimulate the expression of a specific endogenous gene. In principle, any genomic region can be targeted, and recent efforts have successfully generated pooled guide RNA libraries for coding and regulatory regions of human, mouse and Drosophila genomes with high coverage, thus facilitating functional phenotypic screening. In this review, we will highlight recent developments in the area of CRISPR-based functional genomics and discuss potential future directions, with a special focus on mammalian cell systems and arrayed library screening.
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Affiliation(s)
- Alexander Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, London UK
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London UK
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209
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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.
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210
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Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N. Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal 2015; 8:rs9. [PMID: 26350902 PMCID: PMC4642709 DOI: 10.1126/scisignal.aab3729] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The tuberous sclerosis complex (TSC) family of tumor suppressors, TSC1 and TSC2, function together in an evolutionarily conserved protein complex that is a point of convergence for major cell signaling pathways that regulate mTOR complex 1 (mTORC1). Mutation or aberrant inhibition of the TSC complex is common in various human tumor syndromes and cancers. The discovery of novel therapeutic strategies to selectively target cells with functional loss of this complex is therefore of clinical relevance to patients with nonmalignant TSC and those with sporadic cancers. We developed a CRISPR-based method to generate homogeneous mutant Drosophila cell lines. By combining TSC1 or TSC2 mutant cell lines with RNAi screens against all kinases and phosphatases, we identified synthetic interactions with TSC1 and TSC2. Individual knockdown of three candidate genes (mRNA-cap, Pitslre, and CycT; orthologs of RNGTT, CDK11, and CCNT1 in humans) reduced the population growth rate of Drosophila cells lacking either TSC1 or TSC2 but not that of wild-type cells. Moreover, individual knockdown of these three genes had similar growth-inhibiting effects in mammalian TSC2-deficient cell lines, including human tumor-derived cells, illustrating the power of this cross-species screening strategy to identify potential drug targets.
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Affiliation(s)
| | - Alexander J Valvezan
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Colleen Kelley
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Richelle Sopko
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Roesel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shuailiang Lin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Buckner
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rong Tao
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bahar Yilmazel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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211
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Luft C, Ketteler R. Electroporation Knows No Boundaries: The Use of Electrostimulation for siRNA Delivery in Cells and Tissues. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:932-42. [PMID: 25851034 PMCID: PMC4543902 DOI: 10.1177/1087057115579638] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/04/2014] [Accepted: 03/10/2015] [Indexed: 12/15/2022]
Abstract
The discovery of RNA interference (RNAi) has enabled several breakthrough discoveries in the area of functional genomics. The RNAi technology has emerged as one of the major tools for drug target identification and has been steadily improved to allow gene manipulation in cell lines, tissues, and whole organisms. One of the major hurdles for the use of RNAi in high-throughput screening has been delivery to cells and tissues. Some cell types are refractory to high-efficiency transfection with standard methods such as lipofection or calcium phosphate precipitation and require different means. Electroporation is a powerful and versatile method for delivery of RNA, DNA, peptides, and small molecules into cell lines and primary cells, as well as whole tissues and organisms. Of particular interest is the use of electroporation for delivery of small interfering RNA oligonucleotides and clustered regularly interspaced short palindromic repeats/Cas9 plasmid vectors in high-throughput screening and for therapeutic applications. Here, we will review the use of electroporation in high-throughput screening in cell lines and tissues.
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Affiliation(s)
- Christin Luft
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
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212
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Baumert TF, Verrier ER, Nassal M, Chung RT, Zeisel MB. Host-targeting agents for treatment of hepatitis B virus infection. Curr Opin Virol 2015; 14:41-6. [PMID: 26262886 DOI: 10.1016/j.coviro.2015.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/16/2015] [Accepted: 07/20/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) infection is a major cause of chronic liver disease, including liver cirrhosis, liver failure and hepatocellular carcinoma (HCC)-the second leading and fastest rising cause of cancer death world-wide. While de novo infection can be efficiently prevented by vaccination and chronic infection can be controlled using antivirals targeting the viral polymerase, the development of efficient antiviral strategies to eliminate the virus and thus to cure infection remains a key unmet medical need. The recent progress in the development of robust infectious HBV cell culture models now enables the investigation of the full viral life cycle, including a more detailed study of the molecular mechanisms of virus-host interactions responsible for viral persistence. The understanding of these virus-host interactions will be instrumental for the development of curative treatments. Host-dependency factors have recently emerged as promising candidates to treat and prevent infection by various pathogens. This review focuses on the potential of host-targeting agents (HTAs) as novel antivirals to treat and cure HBV infection. These include HTAs that inhibit de novo and re-infection, synthesis and spread of cccDNA as well as development of immune-based approaches eliminating or curing infected hepatocytes, including the eradication of viral cccDNA.
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Affiliation(s)
- Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France; Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000 Strasbourg, France; Liver Center and Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States.
| | - Eloi R Verrier
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Michael Nassal
- Department of Internal Medicine 2/Molecular Biology, University Hospital Freiburg, D-79106 Freiburg, Germany
| | - Raymond T Chung
- Liver Center and Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Mirjam B Zeisel
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France
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213
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Abstract
The most widely used approach for defining gene function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools--specifically CRISPR-based technologies--have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: "Which technology should I use in my experiment?" This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.
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Affiliation(s)
- Michael Boettcher
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA.
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214
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Child HW, Hernandez Y, Conde J, Mullin M, Baptista P, de la Fuente JM, Berry CC. Gold nanoparticle-siRNA mediated oncogene knockdown at RNA and protein level, with associated gene effects. Nanomedicine (Lond) 2015; 10:2513-25. [DOI: 10.2217/nnm.15.95] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aims: RNAi is a powerful tool for gene silencing that can be used to reduce undesirable overexpression of oncogenes as a novel form of cancer treatment. However, when using RNAi as a therapeutic tool there is potential for associated gene effects. This study aimed to utilize gold nanoparticles to deliver siRNA into HeLa cells. Results: Knockdown of the c-myc oncogene by RNAi, at the RNA, protein and cell proliferation level was achieved, while also identifying associated gene responses. Discussion: The gold nanoparticles used in this study present an excellent delivery platform for siRNA, but do note associated gene changes. Conclusion: The study highlights the need to more widely assess the cell physiological response to RNAi treatment, rather than focus on the immediate RNA levels.
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Affiliation(s)
| | - Yulán Hernandez
- Instituto de Nanociencia de Aragón, University of Zaragoza, C/Mariano Esquillor s/n Zaragoza, Spain
| | - João Conde
- Massachusetts Institute of Technology, Institute for Medical Engineering & Science, Harvard-MIT Division for Health Sciences & Technology, Cambridge, MA 02139-4307, USA
| | - Margaret Mullin
- Integrated Microscopy Facility, Joseph Black Building, Glasgow University, G12 8QQ, UK
| | - Pedro Baptista
- UCIBIO, CIGMH, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Portugal
| | - Jesus Maria de la Fuente
- Instituto de Nanociencia de Aragón, University of Zaragoza, C/Mariano Esquillor s/n Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón (ICMA), CSIC-Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009 Zaragoza, Spain
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215
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Abstract
The rise in the prevalence of neurodegenerative diseases parallels the rapid increase in human lifespan. Despite intensive research, the molecular and cellular mechanisms underlying the onset and progression of these devastating diseases with age are still poorly understood. Many aspects of these diseases have been modelled successfully in experimental animals such as the mouse, the zebrafish Brachydanio rero, the nematode worm Caenorhaditis elegans and the fruit fly Drosophila melanogaster. This review will focus on the advantages offered by the genetic tools available in Drosophila for combining powerful strategies in order to tackle the causative factors of these complex pathologies and help to elaborate efficient drugs to treat them.
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Affiliation(s)
- Jean-Antoine Lepesant
- Institut Jacques-Monod, CNRS UMR 7592, Université Paris-Diderot, 15, rue Hélène-Brion, 75205 Paris cedex 13, France.
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216
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Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. G3-GENES GENOMES GENETICS 2015. [PMID: 26199285 PMCID: PMC4555228 DOI: 10.1534/g3.115.019364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA binding proteins (RBPs) are involved in many cellular functions. To facilitate functional characterization of RBPs, we generated an RNA interference (RNAi) library for Drosophila cell-based screens comprising reagents targeting known or putative RBPs. To test the quality of the library and provide a baseline analysis of the effects of the RNAi reagents on viability, we screened the library using a total ATP assay and high-throughput imaging in Drosophila S2R+ cultured cells. The results are consistent with production of a high-quality library that will be useful for functional genomics studies using other assays. Altogether, we provide resources in the form of an initial curated list of Drosophila RBPs; an RNAi screening library we expect to be used with additional assays that address more specific biological questions; and total ATP and image data useful for comparison of those additional assay results with fundamental information such as effects of a given reagent in the library on cell viability. Importantly, we make the baseline data, including more than 200,000 images, easily accessible online.
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217
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Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE. Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS One 2015. [PMID: 26197079 PMCID: PMC4511418 DOI: 10.1371/journal.pone.0131370] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA interference and morphological profiling-the measurement of thousands of phenotypes from individual cells by microscopy and image analysis-are a potentially powerful combination. We show that morphological profiles of RNAi-induced knockdown using the Cell Painting assay are in fact highly sensitive and reproducible. However, we find that the magnitude and prevalence of off-target effects via the RNAi seed-based mechanism make morphological profiles of RNAi reagents targeting the same gene look no more similar than reagents targeting different genes. Pairs of RNAi reagents that share the same seed sequence produce image-based profiles that are much more similar to each other than profiles from pairs designed to target the same gene, a phenomenon previously observed in small-scale gene-expression profiling experiments. Various strategies have been used to enrich on-target versus off-target effects in the context of RNAi screening where a narrow set of phenotypes are measured, mostly based on comparing multiple sequences targeting the same gene; however, new approaches will be needed to make RNAi morphological profiling (that is, comparing multi-dimensional phenotypes) viable. We have shared our raw data and computational pipelines to facilitate research.
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Affiliation(s)
- Shantanu Singh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Xiaoyun Wu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Vebjorn Ljosa
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Mark-Anthony Bray
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - David E. Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - John G. Doench
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Anne E. Carpenter
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail:
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218
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Guo J, McKenna SL, O’Dwyer ME, Cahill MR, O’Driscoll CM. RNA interference for multiple myeloma therapy: targeting signal transduction pathways. Expert Opin Ther Targets 2015; 20:107-21. [DOI: 10.1517/14728222.2015.1071355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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219
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Arbore R, Sekii K, Beisel C, Ladurner P, Berezikov E, Schärer L. Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits. Front Zool 2015; 12:14. [PMID: 26146508 PMCID: PMC4490696 DOI: 10.1186/s12983-015-0106-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/15/2015] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION RNA interference (RNAi) of trait-specific genes permits the manipulation of specific phenotypic traits ("phenotypic engineering") and thus represents a powerful tool to test trait function in evolutionary studies. The identification of suitable candidate genes, however, often relies on existing functional gene annotation, which is usually limited in emerging model organisms, especially when they are only distantly related to traditional genetic model organisms. A case in point is the free-living flatworm Macrostomum lignano (Lophotrochozoa: Platyhelminthes: Rhabditophora), an increasingly powerful model organism for evolutionary studies of sex in simultaneous hermaphrodites. To overcome the limitation of sparse functional annotation, we have performed a positional RNA-Seq analysis on different body fragments in order to identify organ-specific candidate transcripts. We then performed gene expression (in situ hybridization) and gene function (RNAi) analyses on 23 candidate transcripts, both to evaluate the predictive potential of this approach and to obtain preliminary functional characterizations of these candidate genes. RESULTS We identified over 4000 transcripts that could be expected to show specific expression in different reproductive organs (including testis, ovary and the male and female genital systems). The predictive potential of the method could then be verified by confirming organ-specific expression for several candidate transcripts, some of which yielded interesting trait-specific knock-down phenotypes that can now be followed up in future phenotypic engineering studies. CONCLUSIONS Our positional RNA-Seq analysis represents a highly useful resource for the identification of candidate transcripts for functional and phenotypic engineering studies in M. lignano, and it has already been used successfully in several studies. Moreover, this approach can overcome some inherent limitations of homology-based candidate selection and thus should be applicable to a broad range of emerging model organisms.
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Affiliation(s)
- Roberto Arbore
- />Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Kiyono Sekii
- />Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | | | - Peter Ladurner
- />Institute of Zoology and CMBI, University of Innsbruck, Innsbruck, Austria
| | - Eugene Berezikov
- />ERIBA, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas Schärer
- />Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
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Taylor J, Woodcock S. A Perspective on the Future of High-Throughput RNAi Screening: Will CRISPR Cut Out the Competition or Can RNAi Help Guide the Way? ACTA ACUST UNITED AC 2015; 20:1040-51. [PMID: 26048892 DOI: 10.1177/1087057115590069] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/11/2015] [Indexed: 12/18/2022]
Abstract
For more than a decade, RNA interference (RNAi) has brought about an entirely new approach to functional genomics screening. Enabling high-throughput loss-of-function (LOF) screens against the human genome, identifying new drug targets, and significantly advancing experimental biology, RNAi is a fast, flexible technology that is compatible with existing high-throughput systems and processes; however, the recent advent of clustered regularly interspaced palindromic repeats (CRISPR)-Cas, a powerful new precise genome-editing (PGE) technology, has opened up vast possibilities for functional genomics. CRISPR-Cas is novel in its simplicity: one piece of easily engineered guide RNA (gRNA) is used to target a gene sequence, and Cas9 expression is required in the cells. The targeted double-strand break introduced by the gRNA-Cas9 complex is highly effective at removing gene expression compared to RNAi. Together with the reduced cost and complexity of CRISPR-Cas, there is the realistic opportunity to use PGE to screen for phenotypic effects in a total gene knockout background. This review summarizes the exciting development of CRISPR-Cas as a high-throughput screening tool, comparing its future potential to that of well-established RNAi screening techniques, and highlighting future challenges and opportunities within these disciplines. We conclude that the two technologies actually complement rather than compete with each other, enabling greater understanding of the genome in relation to drug discovery.
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Affiliation(s)
- Jessica Taylor
- Global HTS Centre, Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
| | - Simon Woodcock
- Global HTS Centre, Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
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221
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Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes. Sci Rep 2015; 5:10889. [PMID: 26039571 PMCID: PMC4650632 DOI: 10.1038/srep10889] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/22/2015] [Indexed: 01/14/2023] Open
Abstract
Genome-wide transcriptome profiling after gene perturbation is a powerful means of elucidating gene functional mechanisms in diverse contexts. The comprehensive collection and analysis of the resulting transcriptome profiles would help to systematically characterize context-dependent gene functional mechanisms and conduct experiments in biomedical research. To this end, we collected and curated over 3000 transcriptome profiles in human and mouse from diverse gene perturbation experiments, which involved 1585 different perturbed genes (microRNAs, lncRNAs and protein-coding genes) across 1170 different cell lines/tissues. For each profile, we identified differential genes and their associated functions and pathways, constructed perturbation networks, predicted transcription regulation and cancer/drug associations, and assessed cooperative perturbed genes. Based on these transcriptome analyses, the Gene Perturbation Atlas (GPA) can be used to detect (i) novel or cell-specific functions and pathways affected by perturbed genes, (ii) protein interactions and regulatory cascades affected by perturbed genes, and (iii) perturbed gene-mediated cooperative effects. The GPA is a user-friendly database to support the rapid searching and exploration of gene perturbations. Particularly, we visualized functional effects of perturbed genes from multiple perspectives. In summary, the GPA is a valuable resource for characterizing gene functions and regulatory mechanisms after single-gene perturbations. The GPA is freely accessible at http://biocc.hrbmu.edu.cn/GPA/.
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222
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Application guide for omics approaches to cell signaling. Nat Chem Biol 2015; 11:387-97. [DOI: 10.1038/nchembio.1809] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/31/2015] [Indexed: 01/18/2023]
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223
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Dobbelstein M, Sørensen CS. Exploiting replicative stress to treat cancer. Nat Rev Drug Discov 2015; 14:405-23. [PMID: 25953507 DOI: 10.1038/nrd4553] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells and ultimately inducing the catastrophic failure of proliferative machineries. In this Review, we outline current and future approaches to achieve this, emphasizing the combination of conventional chemotherapy with targeted approaches.
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Affiliation(s)
- Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, Ernst Caspari Haus, University of Göttingen, 37077 Göttingen, Germany
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224
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Abstract
Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.
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Affiliation(s)
- Ophir Shalem
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Neville E Sanjana
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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225
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Crotty S, Pipkin ME. In vivo RNAi screens: concepts and applications. Trends Immunol 2015; 36:315-22. [PMID: 25937561 DOI: 10.1016/j.it.2015.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 11/17/2022]
Abstract
Functional genomics approaches that leverage the RNAi pathway have been applied in vivo to examine the roles of hundreds or thousands of genes; mainly in the context of cancer. Here, we discuss principles guiding the design of RNAi screens, parameters that determine success and recent developments that have improved accuracy and expanded the applicability of these approaches to other in vivo settings, including the immune system. We review recent studies that have applied in vivo RNAi screens in T cells to examine genes that regulate T cell differentiation during viral infection, and that control their accumulation in tumors in a model of adoptive T cell therapy. In this context, we put forward an argument as to why RNAi approaches in vivo are likely to provide particularly salient insight into immunology.
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Affiliation(s)
- Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Matthew E Pipkin
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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226
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Barrangou R, Birmingham A, Wiemann S, Beijersbergen RL, Hornung V, Smith AVB. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res 2015; 43:3407-19. [PMID: 25800748 PMCID: PMC4402539 DOI: 10.1093/nar/gkv226] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/05/2015] [Indexed: 12/26/2022] Open
Abstract
The discovery that the machinery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 bacterial immune system can be re-purposed to easily create deletions, insertions and replacements in the mammalian genome has revolutionized the field of genome engineering and re-invigorated the field of gene therapy. Many parallels have been drawn between the newly discovered CRISPR-Cas9 system and the RNA interference (RNAi) pathway in terms of their utility for understanding and interrogating gene function in mammalian cells. Given this similarity, the CRISPR-Cas9 field stands to benefit immensely from lessons learned during the development of RNAi technology. We examine how the history of RNAi can inform today's challenges in CRISPR-Cas9 genome engineering such as efficiency, specificity, high-throughput screening and delivery for in vivo and therapeutic applications.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Stefan Wiemann
- Division of Molecular Genome Analysis, and Genomic & Proteomics Core Facility, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Veit Hornung
- Institute of Molecular Medicine, University Hospital, University of Bonn, 53128 Bonn, Germany
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227
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Hatzihristidis T, Desai N, Hutchins AP, Meng TC, Tremblay ML, Miranda-Saavedra D. A Drosophila-centric view of protein tyrosine phosphatases. FEBS Lett 2015; 589:951-66. [PMID: 25771859 DOI: 10.1016/j.febslet.2015.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 12/30/2022]
Abstract
Most of our knowledge on protein tyrosine phosphatases (PTPs) is derived from human pathologies and mouse knockout models. These models largely correlate well with human disease phenotypes, but can be ambiguous due to compensatory mechanisms introduced by paralogous genes. Here we present the analysis of the PTP complement of the fruit fly and the complementary view that PTP studies in Drosophila will accelerate our understanding of PTPs in physiological and pathological conditions. With only 44 PTP genes, Drosophila represents a streamlined version of the human complement. Our integrated analysis places the Drosophila PTPs into evolutionary and functional contexts, thereby providing a platform for the exploitation of the fly for PTP research and the transfer of knowledge onto other model systems.
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Affiliation(s)
- Teri Hatzihristidis
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Nikita Desai
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hutchins
- Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Tzu-Ching Meng
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Michel L Tremblay
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
| | - Diego Miranda-Saavedra
- World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan; Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain; IE Business School, IE University, María de Molina 31 bis, 28006 Madrid, Spain.
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228
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Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ. A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila. J Genet Genomics 2015; 42:141-9. [PMID: 25953352 DOI: 10.1016/j.jgg.2015.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 12/13/2022]
Abstract
The last couple of years have witnessed an explosion in development of CRISPR-based genome editing technologies in cell lines as well as in model organisms. In this review, we focus on the applications of this popular system in Drosophila. We discuss the effectiveness of the CRISPR/Cas9 systems in terms of delivery, mutagenesis detection, parameters affecting efficiency, and off-target issues, with an emphasis on how to apply this powerful tool to characterize gene functions.
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Affiliation(s)
- Jiang Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua Fly Center, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xia Wang
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Huan-Huan Qiao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo-Wen Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua Fly Center, Tsinghua University, Beijing 100084, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China.
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229
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Porcelli D, Butlin RK, Gaston KJ, Joly D, Snook RR. The environmental genomics of metazoan thermal adaptation. Heredity (Edinb) 2015; 114:502-14. [PMID: 25735594 PMCID: PMC4815515 DOI: 10.1038/hdy.2014.119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 01/07/2023] Open
Abstract
Continued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die', regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.
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Affiliation(s)
- D Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - R K Butlin
- 1] Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK [2] Sven Lovén Centre-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - K J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - D Joly
- 1] Laboratoire Evolution, Génomes et Spéciation, CNRS-UPR 9034, Gif sur Yvette, France [2] Université Paris-Sud, Orsay, France
| | - R R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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230
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Meier R, Mazelier M, Lozach PY. Criblages à haut débit d’ARN interférents. Med Sci (Paris) 2015; 31:247-9. [DOI: 10.1051/medsci/20153103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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231
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Abstract
Many of the major discoveries in the fields of genetics and developmental biology have been made using the fruit fly, Drosophila melanogaster. With regard to heart development, the conserved network of core cardiac transcription factors that underlies cardiogenesis has been studied in great detail in the fly, and the importance of several signaling pathways that regulate heart morphogenesis, such as Slit/Robo, was first shown in the fly model. Recent technological advances have led to a large increase in the genomic data available from patients with congenital heart disease (CHD). This has highlighted a number of candidate genes and gene networks that are potentially involved in CHD. To validate genes and genetic interactions among candidate CHD-causing alleles and to better understand heart formation in general are major tasks. The specific limitations of the various cardiac model systems currently employed (mammalian and fish models) provide a niche for the fly model, despite its evolutionary distance to vertebrates and humans. Here, we review recent advances made using the Drosophila embryo that identify factors relevant for heart formation. These underline how this model organism still is invaluable for a better understanding of CHD.
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232
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Shen H, McHale CM, Smith MT, Zhang L. Functional genomic screening approaches in mechanistic toxicology and potential future applications of CRISPR-Cas9. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:31-42. [PMID: 26041264 DOI: 10.1016/j.mrrev.2015.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 01/25/2023]
Abstract
Characterizing variability in the extent and nature of responses to environmental exposures is a critical aspect of human health risk assessment. Chemical toxicants act by many different mechanisms, however, and the genes involved in adverse outcome pathways (AOPs) and AOP networks are not yet characterized. Functional genomic approaches can reveal both toxicity pathways and susceptibility genes, through knockdown or knockout of all non-essential genes in a cell of interest, and identification of genes associated with a toxicity phenotype following toxicant exposure. Screening approaches in yeast and human near-haploid leukemic KBM7 cells have identified roles for genes and pathways involved in response to many toxicants but are limited by partial homology among yeast and human genes and limited relevance to normal diploid cells. RNA interference (RNAi) suppresses mRNA expression level but is limited by off-target effects (OTEs) and incomplete knockdown. The recently developed gene editing approach called clustered regularly interspaced short palindrome repeats-associated nuclease (CRISPR)-Cas9, can precisely knock-out most regions of the genome at the DNA level with fewer OTEs than RNAi, in multiple human cell types, thus overcoming the limitations of the other approaches. It has been used to identify genes involved in the response to chemical and microbial toxicants in several human cell types and could readily be extended to the systematic screening of large numbers of environmental chemicals. CRISPR-Cas9 can also repress and activate gene expression, including that of non-coding RNA, with near-saturation, thus offering the potential to more fully characterize AOPs and AOP networks. Finally, CRISPR-Cas9 can generate complex animal models in which to conduct preclinical toxicity testing at the level of individual genotypes or haplotypes. Therefore, CRISPR-Cas9 is a powerful and flexible functional genomic screening approach that can be harnessed to provide unprecedented mechanistic insight in the field of modern toxicology.
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Affiliation(s)
- Hua Shen
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Cliona M McHale
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Martyn T Smith
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Luoping Zhang
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA.
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233
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Abstract
Targeted therapies in personalized medicine require the knowledge about the molecular changes within the patient that cause the disease. With the beginning of the new century, a plethora of new technologies became available to detect these changes and use this information as starting point for drug development. Next-generation genome sequencing and sophisticated genome-wide functional genomics' methods have led to a significant increase in the identification of novel drug target candidates and understanding of the relevance of these genomic and molecular changes for the diseases. As functional genomic tool for target identification, high-throughput gene silencing through RNA interference screening has become the established method. RNAi is discussed with its advantages and challenges in this chapter. Furthermore the potential of CRISPR/Cas9, a gene-editing method that has recently been adapted for use as functional screening tool, will be briefly reviewed.
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