- Email: [email protected]
Enabling the Next 25 Years of Cell Biology
TICB 1291 No. of Pages 3
Special Issue: Future of Cell [2_TD$IF]Biology
Editorial
Enabling the Next 25 Years of Cell Biology Jim Woodgett1,@ and Danielle T. Loughlin2,@,* Imagine a time when every lab did not have a PCR machine, genome-editing tools, such as CRISPR/Cas9 did not exist, whole-genome sequencing took years, and fluorescent microscopes were only just becoming commercialized. Doing quality science under these conditions seems archaic, right? While the adaptation of new tools for simple and affordable use has increased the speed of research and perhaps our own ignorance to such advances, looking back 25 years reveals just how far we have come. Cell biologists have visualized most subcellular structures and have created an inventory of molecular components. These paradigm shifts in our knowledge of the cell could only be realized with help from technological advances. Therefore, we end our 25th anniversary with a special issue of Trends in Cell Biology that highlights the technological innovations that will enable the future of cell biology research. The development of the next generation of tools will empower us for the next chapter of discovery: revealing the operational strategies of living cells. When considering tools that have advanced the field, one cannot mention cell biology without also referring to microscopy. Indeed, cell biology as a specialty owes its existence to the development of the microscope. While early developments of this instrument provided us with some of the first glimpses of cells, it was not until modern electron and confocal scanning microscopy became mainstream during the 1980s that resolution at the nanometer level was able to discern delicate cellular architecture. There has been a seemingly continual stream of significant advances in microscopy ever since, including spinning disk, deconvolution, and twophoton microscopy, each providing increased precision, clarity, and depth of range and facilitating ever greater accuracy in the visualization and definition of cellular structures. Super-resolution microscopy tools break the diffraction limit and provide unprecedented resolution within a biologically critical range, enabling the dissection of macrostructures within the cell, such as the centrosome and [3_TD$IF]kinetochore. In other words, these technologies have closed the visual gap between macromolecules that can be structurally determined by crystallography, transmission electron microscopy[4_TD$IF], and light microscopy. Of course, this previously ill-defined space is now being illuminated by rapid developments in cryo-electron microscopy, allowing for a more complete spectrum of cellular definition from molecules to macromolecular complexes. Among the different cryo-electron microscopy tools available is cryo-tomography. Martin Beck and Wolfgang Baumeister discuss how cryo-tomography is beginning to attain near-atomic resolution of multiprotein assemblies. New techniques and optical methods, such as FRET, FLIM, and TIRF, have introduced a degree of quantitative analysis to what had previously been a largely descriptive modality. Today, advances in force microscopy methods have enabled the study of molecular piconewton-scale mechanics within living cells. Carsten Grashoff and colleagues introduce the concepts behind FRET-based tension sensors and discuss their potential in understanding how cells sense and transmit mechanical information. Light can also be used to manipulate cellular functions through
Trends in Cell Biology, Month Year, Vol. xx, No. yy
1 Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, ONT M5G 1X5, Canada 2 Editor, Trends in Cell Biology
*Correspondence: [email protected] (D.T. Loughlin). @ Twitter: @jwoodgett @ Twitter: @TrendsCellBio
http://dx.doi.org/10.1016/j.tcb.2016.09.009 © 2016 Elsevier Ltd. All rights reserved.
1
TICB 1291 No. of Pages 3
genetically encoded light-responsive proteins of the cell. These optogenetic tools, first developed for use in neurons, have been extended to understand the spatiotemporal dynamics in a range of cellular and developmental processes. Stefano De Renzis and colleagues describe the impact optogenetics has, and will continue to have, on understanding cell morphogenesis. A second major technological enabler for cell biology has been live cell imaging. Indeed, we were saddened to hear of the recent premature passing of Roger Tsien, who enabled so much of this field through his revolutionary work on fluorescent proteins. Whereas early advances in light microscopy were primarily applied to snapshots of states in fixed, dead cells, the emergence of high-resolution imaging of live cells over a period of hours or days literally reveals a fourth dimension of cell biology. Jacky Goetz and colleagues describe the advantages of combining intravital imaging of animals with electron microscopy termed ‘intravital-correlative light[1_TD$IF] and electron microscopy[5_TD$IF]', for understanding cell processes in vivo. While the microscope remains the workhorse for much of cell biology, imaging only tells part of the story. Scientists soon realized that our understanding of how a cell works could be greatly facilitated through proteomic analysis. In addition to new optics, the dawn of molecular biology and the development of more advanced biochemical and biophysical tools allowed scientists to build a molecular parts list of the visualized structures, but many of these complexes are refractory to traditional isolation methods. Recent approaches in proximity labeling have been developed to inventory proteins in these restricted compartments or regions of cells. Dae In Kim and Kyle Roux review how these labeling methods are providing maps and histories of the proteomes of subcellular complexes. Going a step further, Georg Kustatscher and Juri Rappsilber describe how machine learning can extend the reach of traditional proteomics and be used to identify potential functions of proteins with fuzzy cellular locations. It is breathtaking to observe how quickly technologies based on sequence-specific targeting, as initially validated via CRISPR engineering, entered and now pervade biological investigations. While editing of genes, per se, including their inactivation and substitution of amino acid variations, will form the mainstay of gene editing, we are only at the dawn of new applications for gRNA/Cas9-mediated manipulations. It does not take much imagination to envisage laser light triggering of events at precise loci (DNA damage responses, induced failures of checkpoints, etc.). Moreover, complex gene editing is becoming more selective and efficient with multiple instances of genome-wide CRISPR screens demonstrating not only feasibility, but also qualitative advantages over RNA suppression. This technology is also entirely transferable to animals and has already become the default methodology for creating new models in multiple species. Fangyuan Wang and Stanley Qi provide an overview of the potential applications of CRISPR/Cas9 technology for cell biology study. Despite these enormous analytical and technical advances, some aspects of cell biology have remained largely unchanged. These are, perhaps, ripe for revolution. Cells are still largely grown in monolayers, typically on tissue culture plastic, and nutrient composition and oxygen levels do not faithfully recapitulate the native environment. Christopher Chen and Donald Ingber outline the progress in 3D culture systems, which can bridge the gap between traditional cell culture and in vivo methods, providing the community with tools to better recapitulate cellular environments. Given the advances in cell culture models, it would seem that there is less of a need to model cell processes in other organisms. However, as Bob Goldstein and Nicole King point out, lessstudied organisms are powerful when used to investigate fundamental biological questions that are not attainable in traditional model systems. In addition, old tools are finding new purposes. Alfred Goldberg discusses how proteasome inhibitors are expanding their utility both as research tools and as therapeutic agents.
2
Trends in Cell Biology, Month Year, Vol. xx, No. yy
TICB 1291 No. of Pages 3
Lastly, it is worth contemplating the changes in the career of cell biologists. Without doubt, today's environment is both more precarious and more challenging. What was once a relatively low-cost field of research has become dependent on expensive new technologies that have hugely advanced capabilities. The price of admission has increased, as have the expectations. Given this new climate, cell biologists need to be creative in how science is both funded and approached. Rick Horwitz outlines how interdisciplinary collaboration and new partnerships with philanthropies can overcome these hurdles to move cell biology forward. By looking back over the past 25 years, it is clear that technological innovations have allowed cell biology to become more precise in its descriptive elements as well as more accurate in its efforts to understand mechanisms. As in many areas of science, the higher the resolution with which we are able to observe, the more we understand and the more we are bewildered by the vast holes in our knowledge. In that sense, cell biology has a secure future. We would like to thank all the authors and reviewers for their contributions to the special issue, and we thank you for reading it. Your comments and ideas are always welcome; you can contact us with feedback or questions at [email protected] or @TrendsCellBio.
Trends in Cell Biology, Month Year, Vol. xx, No. yy
3
Special Issue: Future of Cell [2_TD$IF]Biology
Editorial
Enabling the Next 25 Years of Cell Biology Jim Woodgett1,@ and Danielle T. Loughlin2,@,* Imagine a time when every lab did not have a PCR machine, genome-editing tools, such as CRISPR/Cas9 did not exist, whole-genome sequencing took years, and fluorescent microscopes were only just becoming commercialized. Doing quality science under these conditions seems archaic, right? While the adaptation of new tools for simple and affordable use has increased the speed of research and perhaps our own ignorance to such advances, looking back 25 years reveals just how far we have come. Cell biologists have visualized most subcellular structures and have created an inventory of molecular components. These paradigm shifts in our knowledge of the cell could only be realized with help from technological advances. Therefore, we end our 25th anniversary with a special issue of Trends in Cell Biology that highlights the technological innovations that will enable the future of cell biology research. The development of the next generation of tools will empower us for the next chapter of discovery: revealing the operational strategies of living cells. When considering tools that have advanced the field, one cannot mention cell biology without also referring to microscopy. Indeed, cell biology as a specialty owes its existence to the development of the microscope. While early developments of this instrument provided us with some of the first glimpses of cells, it was not until modern electron and confocal scanning microscopy became mainstream during the 1980s that resolution at the nanometer level was able to discern delicate cellular architecture. There has been a seemingly continual stream of significant advances in microscopy ever since, including spinning disk, deconvolution, and twophoton microscopy, each providing increased precision, clarity, and depth of range and facilitating ever greater accuracy in the visualization and definition of cellular structures. Super-resolution microscopy tools break the diffraction limit and provide unprecedented resolution within a biologically critical range, enabling the dissection of macrostructures within the cell, such as the centrosome and [3_TD$IF]kinetochore. In other words, these technologies have closed the visual gap between macromolecules that can be structurally determined by crystallography, transmission electron microscopy[4_TD$IF], and light microscopy. Of course, this previously ill-defined space is now being illuminated by rapid developments in cryo-electron microscopy, allowing for a more complete spectrum of cellular definition from molecules to macromolecular complexes. Among the different cryo-electron microscopy tools available is cryo-tomography. Martin Beck and Wolfgang Baumeister discuss how cryo-tomography is beginning to attain near-atomic resolution of multiprotein assemblies. New techniques and optical methods, such as FRET, FLIM, and TIRF, have introduced a degree of quantitative analysis to what had previously been a largely descriptive modality. Today, advances in force microscopy methods have enabled the study of molecular piconewton-scale mechanics within living cells. Carsten Grashoff and colleagues introduce the concepts behind FRET-based tension sensors and discuss their potential in understanding how cells sense and transmit mechanical information. Light can also be used to manipulate cellular functions through
Trends in Cell Biology, Month Year, Vol. xx, No. yy
1 Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, ONT M5G 1X5, Canada 2 Editor, Trends in Cell Biology
*Correspondence: [email protected] (D.T. Loughlin). @ Twitter: @jwoodgett @ Twitter: @TrendsCellBio
http://dx.doi.org/10.1016/j.tcb.2016.09.009 © 2016 Elsevier Ltd. All rights reserved.
1
TICB 1291 No. of Pages 3
genetically encoded light-responsive proteins of the cell. These optogenetic tools, first developed for use in neurons, have been extended to understand the spatiotemporal dynamics in a range of cellular and developmental processes. Stefano De Renzis and colleagues describe the impact optogenetics has, and will continue to have, on understanding cell morphogenesis. A second major technological enabler for cell biology has been live cell imaging. Indeed, we were saddened to hear of the recent premature passing of Roger Tsien, who enabled so much of this field through his revolutionary work on fluorescent proteins. Whereas early advances in light microscopy were primarily applied to snapshots of states in fixed, dead cells, the emergence of high-resolution imaging of live cells over a period of hours or days literally reveals a fourth dimension of cell biology. Jacky Goetz and colleagues describe the advantages of combining intravital imaging of animals with electron microscopy termed ‘intravital-correlative light[1_TD$IF] and electron microscopy[5_TD$IF]', for understanding cell processes in vivo. While the microscope remains the workhorse for much of cell biology, imaging only tells part of the story. Scientists soon realized that our understanding of how a cell works could be greatly facilitated through proteomic analysis. In addition to new optics, the dawn of molecular biology and the development of more advanced biochemical and biophysical tools allowed scientists to build a molecular parts list of the visualized structures, but many of these complexes are refractory to traditional isolation methods. Recent approaches in proximity labeling have been developed to inventory proteins in these restricted compartments or regions of cells. Dae In Kim and Kyle Roux review how these labeling methods are providing maps and histories of the proteomes of subcellular complexes. Going a step further, Georg Kustatscher and Juri Rappsilber describe how machine learning can extend the reach of traditional proteomics and be used to identify potential functions of proteins with fuzzy cellular locations. It is breathtaking to observe how quickly technologies based on sequence-specific targeting, as initially validated via CRISPR engineering, entered and now pervade biological investigations. While editing of genes, per se, including their inactivation and substitution of amino acid variations, will form the mainstay of gene editing, we are only at the dawn of new applications for gRNA/Cas9-mediated manipulations. It does not take much imagination to envisage laser light triggering of events at precise loci (DNA damage responses, induced failures of checkpoints, etc.). Moreover, complex gene editing is becoming more selective and efficient with multiple instances of genome-wide CRISPR screens demonstrating not only feasibility, but also qualitative advantages over RNA suppression. This technology is also entirely transferable to animals and has already become the default methodology for creating new models in multiple species. Fangyuan Wang and Stanley Qi provide an overview of the potential applications of CRISPR/Cas9 technology for cell biology study. Despite these enormous analytical and technical advances, some aspects of cell biology have remained largely unchanged. These are, perhaps, ripe for revolution. Cells are still largely grown in monolayers, typically on tissue culture plastic, and nutrient composition and oxygen levels do not faithfully recapitulate the native environment. Christopher Chen and Donald Ingber outline the progress in 3D culture systems, which can bridge the gap between traditional cell culture and in vivo methods, providing the community with tools to better recapitulate cellular environments. Given the advances in cell culture models, it would seem that there is less of a need to model cell processes in other organisms. However, as Bob Goldstein and Nicole King point out, lessstudied organisms are powerful when used to investigate fundamental biological questions that are not attainable in traditional model systems. In addition, old tools are finding new purposes. Alfred Goldberg discusses how proteasome inhibitors are expanding their utility both as research tools and as therapeutic agents.
2
Trends in Cell Biology, Month Year, Vol. xx, No. yy
TICB 1291 No. of Pages 3
Lastly, it is worth contemplating the changes in the career of cell biologists. Without doubt, today's environment is both more precarious and more challenging. What was once a relatively low-cost field of research has become dependent on expensive new technologies that have hugely advanced capabilities. The price of admission has increased, as have the expectations. Given this new climate, cell biologists need to be creative in how science is both funded and approached. Rick Horwitz outlines how interdisciplinary collaboration and new partnerships with philanthropies can overcome these hurdles to move cell biology forward. By looking back over the past 25 years, it is clear that technological innovations have allowed cell biology to become more precise in its descriptive elements as well as more accurate in its efforts to understand mechanisms. As in many areas of science, the higher the resolution with which we are able to observe, the more we understand and the more we are bewildered by the vast holes in our knowledge. In that sense, cell biology has a secure future. We would like to thank all the authors and reviewers for their contributions to the special issue, and we thank you for reading it. Your comments and ideas are always welcome; you can contact us with feedback or questions at [email protected] or @TrendsCellBio.
Trends in Cell Biology, Month Year, Vol. xx, No. yy
3