Enhancing potency of siRNA targeting fusion genes by optimization outside of target sequence.

Canonical siRNA design algorithms have become remarkably effective at predicting favorable binding regions within a target mRNA, but in some cases (e.g., a fusion junction site) region choice is restricted. In these instances, alternative approaches are necessary to obtain a highly potent silencing molecule. Here we focus on strategies for rational optimization of two siRNAs that target the junction sites of fusion oncogenes BCR-ABL and TMPRSS2-ERG. We demonstrate that modifying the termini of these siRNAs with a terminal G-U wobble pair or a carefully selected pair of terminal asymmetry-enhancing mismatches can result in an increase in potency at low doses. Importantly, we observed that improvements in silencing at the mRNA level do not necessarily translate to reductions in protein level and/or cell death. Decline in protein level is also heavily influenced by targeted protein half-life, and delivery vehicle toxicity can confound measures of cell death due to silencing. Therefore, for BCR-ABL, which has a long protein half-life that is difficult to overcome using siRNA, we also developed a nontoxic transfection vector: poly(lactic-coglycolic acid) nanoparticles that release siRNA over many days. We show that this system can achieve effective killing of leukemic cells. These findings provide insights into the implications of siRNA sequence for potency and suggest strategies for the design of more effective therapeutic siRNA molecules. Furthermore, this work points to the importance of integrating studies of siRNA design and delivery, while heeding and addressing potential limitations such as restricted targetable mRNA regions, long protein half-lives, and nonspecific toxicities.

Therapeutic siRNA: principles, challenges, and strategies.

RNA interference (RNAi) is a remarkable endogenous regulatory pathway that can bring about sequence-specific gene silencing. If harnessed effectively, RNAi could result in a potent targeted therapeutic modality with applications ranging from viral diseases to cancer. The major barrier to realizing the full medicinal potential of RNAi is the difficulty of delivering effector molecules, such as small interfering RNAs (siRNAs), in vivo. An effective delivery strategy for siRNAs must address limitations that include poor stability and non-targeted biodistribution, while protecting against the stimulation of an undesirable innate immune response. The design of such a system requires rigorous understanding of all mechanisms involved. This article reviews the mechanistic principles of RNA interference, its potential, the greatest challenges for use in biomedical applications, and some of the work that has been done toward engineering delivery systems that overcome some of the hurdles facing siRNA-based therapeutics.

Glycerol-induced membrane stiffening: the role of viscous fluid adlayers.

Lipid interfaces, ranging from cell membranes to thin surfactant layers that stabilize lung alveoli, are integral to living systems. Such interfaces are often subjected to mechanical forces, and because of their membrane-like geometry, they can easily deform by bending into localized folds. In this work, we explore the role of small molecules (i.e., glycerol) on the mechanical stability of model lung surfactant monolayers. We demonstrate that the presence of glycerol increases local monolayer bending stiffness by orders of magnitude. Our x-ray and neutron reflectivity measurements indicate that water is preferentially depleted, or glycerol is preferentially enriched, at the lipid headgroup/solvent interface, and that this glycerol-enriched layer extends O(10Å) beneath the monolayer with an adsorption free energy of -2.5 to -4.6 kJ/mol. The dramatic change in membrane bending stiffness in the presence of the sugar adlayer is understood in terms of two models: 1), lipid antiplasticization by glycerol; and 2), a continuum mechanical model of the viscous adlayer.

Lateral stress relaxation and collapse in lipid monolayers.

Surfactants at air/water interfaces are often subjected to mechanical stresses as the interfaces they occupy are reduced in area. The most well characterized forms of stress relaxation in these systems are first order phase transitions from lower density to higher density phases. Here we study stress relaxation in lipid monolayers that occurs once chemical phase transitions have been exhausted. At these highly compressed states, the monolayer undergoes global mechanical relaxations termed collapse. By studying four different types of monolayers, we determine that collapse modes are most closely linked to in-plane rigidity. We characterize the rigidity of the monolayer by analyzing in-plane morphology on numerous length scales. More rigid monolayers collapse out-of-plane via a hard elastic mode similar to an elastic membrane, while softer monolayers relax in-plane by shearing.

Tissue-engineered lungs for in vivo implantation.

Because adult lung tissue has limited regeneration capacity, lung transplantation is the primary therapy for severely damaged lungs. To explore whether lung tissue can be regenerated in vitro, we treated lungs from adult rats using a procedure that removes cellular components but leaves behind a scaffold of extracellular matrix that retains the hierarchical branching structures of airways and vasculature. We then used a bioreactor to culture pulmonary epithelium and vascular endothelium on the acellular lung matrix. The seeded epithelium displayed remarkable hierarchical organization within the matrix, and the seeded endothelial cells efficiently repopulated the vascular compartment. In vitro, the mechanical characteristics of the engineered lungs were similar to those of native lung tissue, and when implanted into rats in vivo for short time intervals (45 to 120 minutes) the engineered lungs participated in gas exchange. Although representing only an initial step toward the ultimate goal of generating fully functional lungs in vitro, these results suggest that repopulation of lung matrix is a viable strategy for lung regeneration.