Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly.

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.

Two- and three-input TALE-based AND logic computation in embryonic stem cells.

Biological computing circuits can enhance our ability to control cellular functions and have potential applications in tissue engineering and medical treatments. Transcriptional activator-like effectors (TALEs) represent attractive components of synthetic gene regulatory circuits, as they can be designed de novo to target a given DNA sequence. We here demonstrate that TALEs can perform Boolean logic computation in mammalian cells. Using a split-intein protein-splicing strategy, we show that a functional TALE can be reconstituted from two inactive parts, thus generating two-input AND logic computation. We further demonstrate three-piece intein splicing in mammalian cells and use it to perform three-input AND computation. Using methods for random as well as targeted insertion of these relatively large genetic circuits, we show that TALE-based logic circuits are functional when integrated into the genome of mouse embryonic stem cells. Comparing construct variants in the same genomic context, we modulated the strength of the TALE-responsive promoter to improve the output of these circuits. Our work establishes split TALEs as a tool for building logic computation with the potential of controlling expression of endogenous genes or transgenes in response to a combination of cellular signals.

Designing cell-targeted therapeutic proteins reveals the interplay between domain connectivity and cell binding.

The therapeutic efficacy of cytokines is often hampered by severe side effects due to their undesired binding to healthy cells. One strategy for overcoming this obstacle is to tether cytokines to antibodies or antibody fragments for targeted cell delivery. However, how to modulate the geometric configuration and relative binding affinity of the two domains for optimal activity remains an outstanding question. As a result, many antibody-cytokine complexes do not achieve the desired level of cell-targeted binding and activity. Here, we address these design issues by developing a computational model to simulate the dynamics and binding kinetics of natural and engineered fusion proteins such as antibody-cytokine complexes. To verify the model, we developed a modular system in which an antibody fragment and a cytokine are conjugated via a DNA linker that allows for programmable linker geometry and protein spatial configuration. By assembling and testing several anti-CD20 antibody fragment-interferon ? complexes, we showed that varying the linker length and cytokine binding affinity controlled the magnitude of cell-targeted signaling activation in a manner that agreed with the model predictions, which were expressed as dose-signaling response curves. The simulation results also revealed that there is a range of cytokine binding affinities that would achieve optimal therapeutic efficacy. This rapid prototyping platform will facilitate the rational design of antibody-cytokine complexes for improved therapeutic outcomes.

Cell-matrix interactions in the pathobiology of calcific aortic valve disease: critical roles for matricellular, matricrine, and matrix mechanics cues.

The hallmarks of calcific aortic valve disease (CAVD) are the significant changes that occur in the organization, composition, and mechanical properties of the extracellular matrix (ECM), ultimately resulting in stiffened stenotic leaflets that obstruct flow and compromise cardiac function. Increasing evidence suggests that ECM maladaptations are not simply a result of valve cell dysfunction; they also contribute to CAVD progression by altering cellular and molecular signaling. In this review, we summarize the ECM changes that occur in CAVD. We also discuss examples of how the ECM influences cellular processes by signaling through adhesion receptors (matricellular signaling), by regulating the presentation and availability of growth factors and cytokines to cells (matricrine signaling), and by transducing externally applied forces and resisting cell-generated tractional forces (mechanical signaling) to regulate a wide range of pathological processes, including differentiation, fibrosis, calcification, and angiogenesis. Finally, we suggest areas for future research that should lead to new insights into bidirectional cell-ECM interactions in the aortic valve, their contributions to homeostasis and pathobiology, and possible targets to slow or prevent the progression of CAVD.

ß-catenin mediates mechanically regulated, transforming growth factor-ß1-induced myofibroblast differentiation of aortic valve interstitial cells.

OBJECTIVE: In calcific aortic valve disease, myofibroblasts and activation of the transforming growth factor-ß1 (TGF-ß1) and Wnt/ß-catenin pathways are observed in the fibrosa, the stiffer layer of the leaflet, but their association is unknown. We elucidated the roles of ß-catenin and extracellular matrix stiffness in TGF-ß1-induced myofibroblast differentiation of valve interstitial cells (VICs). METHODS AND RESULTS: TGF-ß1 induced rapid ß-catenin nuclear translocation in primary porcine aortic VICs in vitro through TGF-ß receptor I kinase. Degrading ß-catenin pharmacologically or silencing it with small interfering RNA inhibited TGF-ß1-induced myofibroblast differentiation without altering Smad2/3 activity. Conversely, increasing ß-catenin availability with Wnt3A alone did not induce differentiation. However, combining TGF-ß1 and Wnt3A caused greater myofibroblast differentiation than TGF-ß1 treatment alone. Notably, in VICs grown on collagen-coated PA gels with physiological stiffnesses, TGF-ß1-induced ß-catenin nuclear translocation and myofibroblast differentiation occurred only on matrices with fibrosa-like stiffness, but not ventricularis-like stiffness. In diseased aortic valves from pigs fed an atherogenic diet, myofibroblasts colocalized with increased protein expression of Wnt3A, ß-catenin, TGF-ß1, and phosphorylated Smad2/3 in the fibrosa. CONCLUSIONS: Myofibroblast differentiation of VICs involves matrix stiffness-dependent crosstalk between TGF-ß1 and Wnt signaling pathways and may explain in part why the stiffer fibrosa is more susceptible to disease.

Microfabricated arrays for high-throughput screening of cellular response to cyclic substrate deformation.

Mechanical forces play an important role in regulating cellular function and have been shown to modulate cellular response to other factors in the cellular microenvironment. Presently, no technique exists to rapidly screen for the effects of a range of uniform mechanical forces on cellular function. In this work, we developed and characterized a novel microfabricated array capable of simultaneously applying cyclic equibiaxial substrate strains ranging in magnitude from 2 to 15% to small populations of adherent cells. The array is versatile, and capable of simultaneously generating a range of substrate strain fields and magnitudes. The design can be extended to combinatorially manipulate other mechanobiological culture parameters in the cellular microenvironment. As a first demonstration of this technology, the array was used to determine the effects of equibiaxial mechanical strain on activation of the canonical Wnt/beta-catenin signaling pathway in cardiac valve mesenchymal progenitor cells. This high-throughput approach to mechanobiological screening enabled the identification of a novel co-dependence between strain magnitude and duration of stimulation in controlling beta-catenin nuclear accumulation. More generally, this versatile platform has broad applicability in the fields of mechanobiology, tissue engineering and pathobiology.

Identification and characterization of aortic valve mesenchymal progenitor cells with robust osteogenic calcification potential.

Advanced valvular lesions often contain ectopic mesenchymal tissues, which may be elaborated by an unidentified multipotent progenitor subpopulation within the valve interstitium. The identity, frequency, and differentiation potential of the putative progenitor subpopulation are unknown. The objectives of this study were to determine whether valve interstitial cells (VICs) contain a subpopulation of multipotent mesenchymal progenitor cells, to measure the frequencies of the mesenchymal progenitors and osteoprogenitors, and to characterize the osteoprogenitor subpopulation because of its potential role in calcific aortic valve disease. The multilineage potential of freshly isolated and subcultured porcine aortic VICs was tested in vitro. Progenitor frequencies and self-renewal capacity were determined by limiting dilution and colony-forming unit assays. VICs were inducible to osteogenic, adipogenic, chondrogenic, and myofibrogenic lineages. Osteogenic differentiation was also observed in situ in sclerotic porcine leaflets. Primary VICs had strikingly high frequencies of mesenchymal progenitors (48.0 +/- 5.7%) and osteoprogenitors (44.1 +/- 12.0%). High frequencies were maintained for up to six population doublings, but decreased after nine population doublings to 28.2 +/- 9.9% and 5.8 +/- 1.3%, for mesenchymal progenitors and osteoprogenitors, respectively. We further identified the putative osteoprogenitor subpopulation as morphologically distinct cells that occur at high frequency, self-renew, and elaborate bone matrix from single cells. These findings demonstrate that the aortic valve is rich in a mesenchyma l progenitor cell population that has strong potential to contribute to valve calcification.

Calcification by valve interstitial cells is regulated by the stiffness of the extracellular matrix.

OBJECTIVE: Extensive remodeling of the valve ECM in calcific aortic valve sclerosis alters its mechanical properties, but little is known about the impact of matrix mechanics on the cells within the valve interstitium. In this study, the influence of matrix stiffness in modulating calcification by valve interstitial cells (VICs), and their differentiation to pathological phenotypes was assessed. METHODS AND RESULTS: Primary porcine aortic VICs were cultured in standard media or calcifying media on constrained type I fibrillar collagen gels. Matrix stiffness was altered by changing only the thickness of the gels. Calcification did not occur in standard media, regardless of matrix stiffness. However, when VICs were grown in calcifying media on relatively compliant matrices with stiffness similar to that of normal tissue, they readily formed calcified aggregates of viable cells that expressed osteoblast-related transcripts and proteins. In contrast, VICs cultured in calcifying media on stiffer matrices (similar to stenotic tissue) differentiated to myofibroblasts and formed calcified aggregates that contained apoptotic cells. Actin depolymerization reduced aggregation on stiff, but not compliant, matrices. TGF-beta1 potentiated aggregate formation on stiff matrices by enhancing alpha-smooth muscle actin expression and cellular contractility, but not on compliant matrices attributable to downregulation of TGF-beta receptor I. Cell contraction by VICs inhibited Akt activation and enhanced apoptosis-dependent calcification on stiff matrices. CONCLUSIONS: Differentiation of VICs to pathological phenotypes in response to biochemical cues is modulated by matrix stiffness. Although osteogenic or myofibrogenic differentiation of VICs can result in calcification, the processes are distinct.

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications.

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies--for example, repeated terminator and insulator sequences--that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

The elastic properties of valve interstitial cells undergoing pathological differentiation.

Increasing evidence indicates that the progression of calcific aortic valve disease (CAVD) is influenced by the mechanical forces experienced by valvular interstitial cells (VICs) embedded within the valve matrix. The ability of VICs to sense and respond to tissue-level mechanical stimuli depends in part on cellular-level biomechanical properties, which may change with disease. In this study, we used micropipette aspiration to measure the instantaneous elastic modulus of normal VICs and of VICs induced to undergo pathological differentiation in vitro to osteoblast or myofibroblast lineages on compliant and stiff collagen gels, respectively. We found that VIC elastic modulus increased after subculturing on stiff tissue culture-treated polystyrene and with pathological differentiation on the collagen gels. Fibroblast, osteoblast, and myofibroblast VICs had distinct cellular-level elastic properties that were not fully explained by substrate stiffness, but were correlated with α-smooth muscle actin expression levels. C-type natriuretic peptide, a peptide expressed in aortic valves in vivo, prevented VIC stiffening in vitro, consistent with its ability to inhibit α-smooth muscle actin expression and VIC pathological differentiation. These data demonstrate that VIC phenotypic plasticity and mechanical adaptability are linked and regulated both biomechanically and biochemically, with the potential to influence the progression of CAVD.

Boning up on Wolff's Law: mechanical regulation of the cells that make and maintain bone.

Bone tissue forms and is remodeled in response to the mechanical forces that it experiences, a phenomenon described by Wolff's Law. Mechanically induced formation and adaptation of bone tissue is mediated by bone cells that sense and respond to local mechanical cues. In this review, the forces experienced by bone cells, the mechanotransduction pathways involved, and the responses elicited are considered. Particular attention is given to two cell types that have emerged as key players in bone mechanobiology: osteocytes, the putative primary mechanosensors in intact bone; and osteoprogenitors, the cells responsible for bone formation and recently implicated in ectopic calcification of cardiovascular tissues. Mechanoregulation of bone involves a complex interplay between these cells, their microenvironments, and other cell types. Thus, dissection of the role of mechanics in regulating bone cell fate and function, and translation of that knowledge to improved therapies, requires identification of relevant cues, multifactorial experimental approaches, and advanced model systems that mimic the mechanobiological environment.