Abstract
On behalf of the JALA Scientific Advisors and JALA Editorial Board members, I am thrilled to present this year’s honorees of the prestigious JALA Ten. For the past 5 years, JALA has highlighted and honored the very best work that each year has to offer across of a wide range of disciplines, including automation, therapeutics, nanotechnology, tissue engineering, and bio-inspired or bio-related computing. Those selected for The JALA Ten have and continue to make incredible breakthroughs in their fields that will have far-reaching impact in our everyday lives, from how we detect and treat diseases to how we manipulate and observe the world around us.
This year’s honorees continue this tradition of groundbreaking research and include a wide range of investigators at various stages in their careers. The work they have done will improve how we do basic research, translational research, clinical therapy, and diagnostics as well as how we design and use computers. For examples, Dr. Chad Mirkin’s laboratory at Northwestern University demonstrates that its spherical nucleic acid (SNA) nanoparticles are capable of crossing the blood-brain barrier (BBB) and delivering RNA interference therapy against a difficult-to-treat cancer. This work was highlighted because both effective complex therapeutic delivery across the BBB as well as effective therapeutic delivery of RNA, which is notoriously unstable, are translational hurdles that continue to elude basic researchers and clinicians. The work that Dr. Chad Mirkin’s team is doing will advance our understanding of how to overcome both of these challenges and provides a new method to a difficult treatment approach.
On the other end of the application spectrum, Dr. Dharmendra Modha at IBM and the global SyNAPSE group demonstrate the potential of bio-inspired computing in the form of a single chip that contains 1 million neurons and 256 million configurable synapses. Even more impressive is that this artificial brain-on-a-chip is capable of conducting complex neural processes such as multiobject detection and classification while being made from existing common-use computing technology. This work is just the beginning of a new frontier of neurosynaptic computing that will change the way computers learn, remember, and deliver applications that will improve every aspect of our lives.
Although broad in topic and applications, this year’s honorees reflect JALA’s mission to advance translational laboratory science and technology. Whether it is harnessing nanotechnology to change the way drugs are delivered to the eye for the past 100 years or being able to interrogate protein expression and genomic analysis at the single-cell level, the breakthroughs highlighted in this year’s JALA Ten are shining examples of what can be done when multidisciplinary approaches to translational research occur. The results are nothing short of amazing, and we are proud to be able to honor these groups for their hard work and innovative spirit.
JALA and SLAS would like to thank all the nominators and nominees as well as a group of dedicated individuals who worked tirelessly to discuss and select The 2015 JALA Ten. Each year seems to bring about even more innovation and more breakthroughs, and we are excited to see what the research community comes up with next year.
Spherical Nucleic Acid Nanoparticle RNAi Therapy against Glioblastoma
Spherical nucleic acids, or SNAs, are a revolutionary set of structures consisting of nucleic acids arranged around a nanoparticle core in a highly oriented and densely packed form. SNAs pioneered by Professor Chad Mirkin and his team at Northwestern University in Evanston, Illinois, have significantly advanced the fields of therapeutics, diagnostics, and real-time cellular interrogation, among many others. Recently, Mirkin and colleagues demonstrated that SNAs are capable of crossing the BBB to markedly enhance the safety and efficacy of glioblastoma treatment via RNA interference against antiapoptotic tumor pathways ( Fig. 1 ).
Delivery of spherical nucleic acids across the blood-brain barrier with enhanced uptake in glioma tumor cells. Reprinted with permission from AAAS 2013. Jensen, S. A.; Day, E. S.; Ko, C. H.; et al. Spherical Nucleic Acid Nanoparticle Conjugates as an RNAi-Based Therapy for Glioblastoma. Sci. Transl. Med.
Given the remarkable outcomes of SNA-mediated nanotherapy, Mirkin and colleagues have made major progress toward translating game-changing advances in nanomedicine into the clinic. In addition to therapy, SNAs have already made a profound impact on industry in the area of diagnostics and sensing as the only platforms that are capable of monitoring real-time RNA expression in live cells. These Smartflares, which are also known as Nanoflares, are versatile SNA-based probes that can interrogate gene programs that are associated with cancer, inflammation, and a host of other critical biological pathways. As a demonstration of how these SNAs are forging the impact of nanotechnology from the lab to the clinic, they have been commercialized into more than 1700 products and counting.
Sustainable Drug Release from Therapeutic Contact Lenses with Nanodiamonds
Among the many therapeutic approaches against glaucoma, the use of eye drops containing the drug timolol maleate has been widely used. However, a lack of patient compliance due to the discomfort of tear drop use is a major challenge that can result in treatment complications and blindness. Recently, a team led by Professor Dean Ho at the University of California, Los Angeles, has demonstrated that nanodiamonds can serve as an innovative solution to this problem. Specifically, Ho and colleagues have developed nanodiamond-containing contact lenses that are loaded with timolol ( Fig. 2 ). These lenses are capable of triggering timolol release upon interacting with lysozyme, an enzyme that is found in tears.
Model of nanodiamond-nanogel drug delivery in contact lenses. Reprinted with permission from ACS Nano 2014. Kim, H. J.; Zhang, K.; Moore, L.; et al. Diamond Nanogel-Embedded Contact Lenses Mediate Lysozyme-Dependent Therapeutic Release. ACS Nano.
Ho’s work has previously pioneered the use of nanodiamonds to deliver several classes of drugs and imaging compounds. During the course of these studies, the ability of nanodiamonds to coordinate water molecules around their uniquely faceted surfaces emerged as a mechanism that accounted for the remarkable improvements in therapeutic and imaging efficacy. This same mechanism serves as a powerful foundation for the use of nanodiamonds in contact lenses.
The nanodiamond contact lens properties enable lysozyme contact with the drug-loaded diamond particles within the lenses to trigger drug release and also maintain adequate water content and oxygen permeability that ensures wear comfort for future users. In addition to the fields of cancer and regenerative medicine, ophthalmology is a newly proven area in which nanodiamonds may have a big impact.
Mapping Photothermally Induced Gene Expression in Living Cells and Tissues by Nanorod-Locked Nucleic Acid Complexes
Single-cell gene expression analysis has opened new opportunities in elucidating various biological and translational problems. High-throughput single-cell gene expression analysis in the native tissue environment, however, remains a challenging task. Using a gold nanorod-locked nucleic acid probe (GNR-LNA), Professor Pak Kin Wong and his group from the University of Arizona in Tucson report dynamic monitoring of gene expression in viable tissues ( Fig. 3 ). The GNR binds spontaneously to the LNA probes to form GNR-LNA complex and quenches the fluorophore. The GNR allows endocytic delivery of the LNA probes into tissues and hybridizes specifically to the target mRNA, allowing the fluorophore to fluoresce. This technique enables characterization of heterogeneity in cancer tissues and mapping of spatiotemporal cell response during development and regeneration.
Model of gold nanorod-locked nucleic acid probe–mediated dynamic monitoring of gene expression. Reprinted with permission from ACS Nano 2014. Riahi, R.; Wang, S.; Long, M.; et al. Mapping Photothermally Induced Gene Expression in Living Cells and Tissues by Nanorod-Locked Nucleic Acid Complexes. ACS Nano.
Designer Protein Cage Made of a Single Polypeptide: A Step Further toward Artificial Compartments
Biological molecules have the inherent ability to self-assemble and form higher-order nanostructures with high precision, for example, virus capsids and protein cages. Rational design to mimic the natural self-assembly process results in artificial structures. A well-known example is DNA base-pairing that gives rise to DNA origami and more recently coiled-coil peptide dimerization that makes protein origami possible. Stemming from an entry for the International Genetically Engineered Machine (iGEM) competition in 2009, Roman Jerala’s group at the National Institute of Chemistry in Ljubljana, Slovenia, has designed, developed, and constructed a tetrahedron of ~7 nm from a single-chain polypeptide containing 12 coiled-coil peptide modules ( Fig. 4 ).
Schematic of single-chain polypeptide tetrahedron pathway. Reprinted with permission from Nature Publishing Group 2014. Gradišar, H.; Božicˇ, S.; Doles, T.; et al. Design of a Single-Chain Polypeptide Tetrahedron Assembled from Coiled-Coil Segments. Nat. Chem. Biol.
A pair of coiled-coil peptide modules interacts in parallel or antiparallel orientations, and six pairs of the coiled-coil orthogonal dimers make up the six sides of the tetrahedron. Each 2 of the 12 coiled-coil peptide is separated with tetra-peptide linkers (Ser-Gly-Pro-Gly) that allow formation of flexible hinges at the vertices. The flexibility of the modular coiled-coil building block design lends numerous possibilities to construct other hierarchical structures serving as scaffolds for rationally designed artificial compartments.
Biased Receptor Signaling
Biased receptor signaling is redefining the field of target validation and also reducing new drug candidate attrition due to misconceived profiles of drug efficacy. Biased signaling qualifies as a new mode of drug therapy that conceivably could lead to a decrease in mortality and/or morbidity. Professor Terry Kenakin and colleagues at the University of North Carolina in Chapel Hill are the first to develop models describing how ligands stabilize a wide variety of receptor conformations ( Fig. 5 ).
Representation of biased agonism (a) or antagonism (b). Reprinted with permission from Nature Publishing Group 2014. Kenakin, T.; Christopoulos, A. Signaling Bias in New Drug Discovery: Detection, Quantification and Therapeutic Impact. Nat. Rev. Drug Discov.
This idea has far-reaching implications in that the possibility exists that molecules stabilizing unique G protein–coupled receptor (GPCR) conformations could induce selective signaling beyond that determined by GPCR subtypes (i.e., a new dimension for drug selectivity).
Thermoresponsive Nanofabricated Substratum for Three-Dimensional Tissue Engineering
Current tissue-engineering methods lack the ability to properly re-create scaffold-free tissues with physiological structures. For many tissues, the physiological structure is integral to function. Professor Deok-Ho Kim and his group at the University of Washington in Seattle have developed a platform for three-dimensional (3D) tissue engineering using a thermoresponsive nanofabricated substratum (TNFS) and a gel casting method ( Fig. 6 ). The TNFS and gel casting allow for the structural control of aligned cell monolayers that can be spontaneously detached, transferred without loss of anisotropy, and stacked as multilayered tissues with specific layer orientations. Single sheets and multilayered tissues retain structural anisotropy, allowing for the fabrication of scaffold-free, 3D tissues with hierarchical control of overall tissue structure.
Structural control of aligned cell monolayers using thermoresponsive nanofabricated substratum and gel casting allowing for stacked multilayered three-dimensional tissue. Reprinted with permission from ACS Nano 2014. Jiao, A.; Trosper, N. E.; Yang, H. S.; et al. Thermoresponsive Nanofabricated Substratum for the Engineering of Three-Dimensional Tissues with Layer-by-Layer Architectural Control. ACS Nano.
Label-Free Enzymatic Activity Assay
The SAMDI method is the first label-free array-based method for assaying enzyme activities in complex samples ( Fig. 7 ). The arrays are prepared by immobilizing peptides to a self-assembled monolayer of alkanethiolates on gold. Application of a cell lysate allows enzymes in the sample to modify peptides within the array. Significantly, the array is analyzed with MALDI-ToF mass spectrometry and reports changes in the masses of the peptides. It therefore identifies enzyme activities that were present in the lysate. The recent article in Analytical Chemistry from Professor Milan Mrksich and his group at Northwestern University in Evanston, Illinois, is the first to demonstrate the suitability of the SAMDI method for analyzing cell lysates and suggests that this method will have a very broad impact in biology and medicine.
SAMDI assay profiling of deacetylase activity using cysteine-terminated polypeptides containing acetylated lysines. Reprinted with permission from Analytical Chemistry 2014. Kuo, H. Y.; DeLuca, T. A.; Miller, W. M.; et al. Profiling Deacetylase Activities in Cell Lysates with Peptide Arrays and SAMDI Mass Spectrometry. Anal. Chem.
Single-Cell Western Blotting
A single-cell Western (scWestern) blotting technique allows quantitative measurements of up to 11 protein targets from ~2000 individual cells in less than 4 h, expanding single-cell heterogeneity studies to the proteome. To expand tools for assessing cell-to-cell heterogeneity to the proteome, Professor Amy E. Herr and her group at the University of California, Berkeley, introduce a single-cell Western blot realized in a microarray-like planar form factor ( Fig. 8 ).
Microarray capable of 420 concurrent single-cell Western blots. Reprinted with permission from Nature Publishing Group 2014. Hughes, A. J.; Spelke, D. P.; Xu, Z.; et al. Single-Cell Western Blotting. Nat. Methods
The tool measures cell-to-cell variation by supporting ~103 concurrent single-cell Western blots in ~4 h. A 30 µm thick photoactive polyacrylamide gel layered on a microscope slide enables settling of single cells into microwells, chemical cell lysis in each well, gel electrophoresis through each microwell wall and into the supporting polyacrylamide gel layer, photo-initiated blotting to immobilize proteins in the photoactive gel, and diffusive-driven antibody probing of the resolved protein peaks. A conventional microarray scanner reads the assay output. This new technique will have a huge impact on the capability of researchers to study proteins at the single-cell level across a wide range of biological applications.
Single-Nucleus Genome Sequencing
There is increasing evidence that genomic diversity within tumors may play a key role in tumor pathogenesis and therapeutic response. Understanding the heterogeneity in genomic alterations within a tumor requires improved methods of single-cell genomic analysis. Professor Nicholas E. Navin and his colleagues at The University of Texas M.D. Anderson Cancer Center in Houston demonstrate a method for single nucleus genome sequencing that reveals that more aggressive breast cancers also have an increased mutation rate compared with less aggressive, more treatable breast cancers ( Fig. 9 ).
Model of clonal evolution in which more aggressive breast cancers have increased mutation rates. Reprinted with permission from Nature Publishing Group 2014. Wang, Y.; Waters, J.; Leung, M. L.; et al. Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing. Nature
This work is an important jump in translational application of single-cell genomic analysis. By using the natural cell cycle of cells in which single cells duplicate their genome during the S phase, the authors are able to isolate enough DNA from a single cell without the use of small-molecule inhibitors. As such, single-cell analysis can be done on frozen tissue samples, in addition to live cells, greatly increasing the clinical feasibility of this technique.
A Scalable Artificial Brain
A major goal of bio-inspired engineering is developing a computer as efficient and complex as our own brains. Dr. Dharmendra S. Modha at IBM in IBM Research-Almaden in San Jose, California, and collaborators in the Systems of Neuromorphic Adaptive Plastic Scalable Electronics (SyNAPSE) program have developed an efficient and scalable von-Neumann architecture that uses existing integrated chip technology to develop an artificial brain chip.
As a proof of concept, the authors built a 5.4 billion transistor chip with 4096 neurosynaptic cores that integrates 1 million spiking neurons and 256 million synapses ( Fig. 10 ). The chip is capable of replicating complex neural network functions, including multiobject detection and classification. This work demonstrates that an artificial brain is not science fiction, and existing technology can be used to develop highly complex brain-inspired neurosynaptic computers.
Network topology map from 5.4 billion transistor chip with 64 of 4096 neurosynaptic cores shown. Reprinted with permission from AAAS 2014. Merolla, P. A.; Arthur, J. V.; Alvarez-Icaza, R.; et al. A Million Spiking-Neuron Integrated Circuit with a Scalable Communication Network and Interface. Science.