Importance of the DNA “bond” in programmable nanoparticle crystallization

If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling’s rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.Materials scientists have accomplished much by studying the way atoms and molecules crystallize. In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3–14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM). These rules allow one to predict the thermodynamically favored structure as the arrangement of particles that maximizes complementary contacts and therefore DNA hybridization (2, 6). These efforts have been very successful in predicting the thermodynamically favored product; recent studies have even demonstrated that PAEs can form single-crystal Wulff polyhedra that are analogous to those formed in atomic systems with the same crystallographic symmetry (15). However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3, 4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.Here, we study the crystallization process and find that the complexity of the polyvalent DNA interactions can be simply understood by considering the behavior of a single DNA bond. By systematically studying the roles of nucleobase sequence, solution ionic strength, DNA density, and temperature on crystallization, we find that the effects of these factors are mirrored by the rates of hybridization and dehybridization of free DNA. In addition to examining steady-state structures, we evaluate the formation and reorganization of these crystals in a time-resolved manner using small-angle X-ray scattering (SAXS) to study how crystallization dynamics are affected by each design variable. Finally, we develop a predictive model that allows one to compare the range of temperatures over which crystallization will occur for different conditions. In addition to providing an avenue for improving PAE crystallization and realizing new architectures, the effectiveness of this reductionist model suggests that this approach can be applied to study crystallization in a broader class of systems, thus making an impact in the materials by design community.     

A common X-linked inborn error of carnitine biosynthesis may be a risk factor for nondysmorphic autism

We recently reported a deletion of exon 2 of the trimethyllysine hydroxylase epsilon (TMLHE) gene in a proband with autism. TMLHE maps to the X chromosome and encodes the first enzyme in carnitine biosynthesis, 6-N-trimethyllysine dioxygenase. Deletion of exon 2 of TMLHE causes enzyme deficiency, resulting in increased substrate concentration (6-N-trimethyllysine) and decreased product levels (3-hydroxy-6-N-trimethyllysine and γ-butyrobetaine) in plasma and urine. TMLHE deficiency is common in control males (24 in 8,787 or 1 in 366) and was not significantly increased in frequency in probands from simplex autism families (9 in 2,904 or 1 in 323). However, it was 2.82-fold more frequent in probands from male-male multiplex autism families compared with controls (7 in 909 or 1 in 130; P = 0.023). Additionally, six of seven autistic male siblings of probands in male-male multiplex families had the deletion, suggesting that TMLHE deficiency is a risk factor for autism (metaanalysis Z-score = 2.90 and P = 0.0037), although with low penetrance (2-4%). These data suggest that dysregulation of carnitine metabolism may be important in nondysmorphic autism; that abnormalities of carnitine intake, loss, transport, or synthesis may be important in a larger fraction of nondysmorphic autism cases; and that the carnitine pathway may provide a novel target for therapy or prevention of autism.     

The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors

CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.     

Three differentiation states risk-stratify bladder cancer into distinct subtypes

Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.     

Coordinated events: FGF signaling and other related pathways in palatogenesis

Cleft palate is a common craniofacial anomaly that is costly to both patients and the health care system. Investigation of each stage of palate development enhances understanding of this anomaly. Although the exact molecular signaling mechanisms that contribute to palatogenesis remain elusive, multiple pathways, such as fibroblast growth factor (FGF) signaling, have been recognized as important contributors. Alterations in FGF signaling have previously been implicated in palatal clefting. The current review discusses FGF signaling and the major signaling mediators affecting FGF signaling during each stage of palatogenesis.     

Immunobiology of face transplantation

Fourteen face transplants have been performed worldwide since the procedure was successfully introduced in 2005. Vascularized composite tissue allotransplantation may now be considered a viable option for the repair of complex craniofacial defects, for which the results of autologus reconstruction remain suboptimal. However, the benefits must be balanced against the risks inherent in major surgery and the adverse effects of lifelong immunosuppression. In this article, we review the current practice and areas of controversy in facial vascularized composite tissue allotransplantation with particular respect to the unique immunobiology of this procedure. We also describe promising recent advances in immunotherapy and tolerance induction strategies that may soon reach clinical application.