Inference for Low-rank Models without Estimating the Rank

This paper studies the inference about linear functionals of high-dimensional low-rank matrices. While most existing inference methods would require consistent estimation of the true rank, our procedure is robust to rank misspecification, making it a promising approach in applications where rank estimation can be unreliable. We estimate the low-rank spaces using pre-specified weighting matrices, known as diversified projections. A novel statistical insight is that, unlike the usual statistical wisdom that overfitting mainly introduces additional variances, the over-estimated low-rank space also gives rise to a non-negligible bias due to an implicit ridge-type regularization. We develop a new inference procedure and show that the central limit theorem holds as long as the pre-specified rank is no smaller than the true rank. Empirically, we apply our method to the U.S. federal grants allocation data and test the existence of pork-barrel politics

Inference for Low-rank Completion without Sample Splitting with Application to Treatment Effect Estimation

This paper studies the inferential theory for estimating low-rank matrices. It also provides an inference method for the average treatment effect as an application. We show that the least square estimation of eigenvectors following the nuclear norm penalization attains the asymptotic normality. The key contribution of our method is that it does not require sample splitting. In addition, this paper allows dependent observation patterns and heterogeneous observation probabilities. Empirically, we apply the proposed procedure to estimating the impact of the presidential vote on allocating the U.S. federal budget to the states

Lactate oxidase/catalase-displaying nanoparticles efficiently consume lactate in the tumor microenvironment to effectively suppress tumor growth

<jats:title>Abstract</jats:title><jats:p>The aggressive proliferation of tumor cells often requires increased glucose uptake and excessive anaerobic glycolysis, leading to the massive production and secretion of lactate to form a unique tumor microenvironment (TME). Therefore, regulating appropriate lactate levels in the TME would be a promising approach to control tumor cell proliferation and immune suppression. To effectively consume lactate in the TME, lactate oxidase (LOX) and catalase (CAT) were displayed onto <jats:italic>Aquifex aeolicus</jats:italic> lumazine synthase protein nanoparticles (AaLS) to form either AaLS/LOX or AaLS/LOX/CAT. These complexes successfully consumed lactate produced by CT26 murine colon carcinoma cells under both normoxic and hypoxic conditions. Specifically, AaLS/LOX generated a large amount of H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> with complete lactate consumption to induce drastic necrotic cell death regardless of culture condition. However, AaLS/LOX/CAT generated residual H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>, leading to necrotic cell death only under hypoxic condition similar to the TME. While the local administration of AaLS/LOX to the tumor site resulted in mice death, that of AaLS/LOX/CAT significantly suppressed tumor growth without any severe side effects. AaLS/LOX/CAT effectively consumed lactate to produce adequate amounts of H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> which sufficiently suppress tumor growth and adequately modulate the TME, transforming environments that are favorable to tumor suppressive neutrophils but adverse to tumor-supportive tumor-associated macrophages. Collectively, these findings showed that the modular functionalization of protein nanoparticles with multiple metabolic enzymes may offer the opportunity to develop new enzyme complex-based therapeutic tools that can modulate the TME by controlling cancer metabolism.</jats:p> <jats:p><jats:bold>Graphical Abstract</jats:bold></jats:p&gt

Development of Multi-functional Protein Nanostructures for Biomedical Applications

Department of Biological SciencesRecent development of construction of nanostructured materials such as nanoparticles, nanowire, and nanosheets has made a great contribution to the advance of our life since they are closely related to the various biomedical applications. Despite the recent advances in technology for constructing complex nanostructured materials, there is still a long way to go to develop more advanced and more sophisticated materials. Construction of nano-sized supramolecules with precise orientation of structures and functions can provide opportunity to develop new materials which can control the complex biological processes. In this study, we used protein cage nanoparticle as the template for the construction of the complex nanostructured materials and utilized them in various biomedical fields. The Aquifex aeolicus lumazine synthase protein cage nanoparticle was engineered to enable post-translational surface modification with various proteins. SpyTag (ST) displayed lumazine synthase forms covalent display of various SpyCatcher (SC) fusion proteins, and those protein cage nanoparticles were utilized as building blocks for the construction of enzyme-containing multi-layered 3D nanoreaction clusters with enhanced enzymatic activity. The Thermotoga maritima encapsulin protein cage nanoparticle, having outer diameter of 24 nm and inner diameter of 20 nm, was engineered for the simultaneous modification of interior space and exterior surface. Introduction of both split intein fragments and ST/SC enabled protein cargo encapsulation and additional ligand decoration, respectively, in a mix-and-match manner. The constructed protein nanostructures were further applied in the enzyme immobilization, multi-layer construction, and targeted cell imaging. Furthermore, previously developed ST displayed lumazine synthase protein cage nanoparticle was utilized as a template for simultaneous immobilization of the potential therapeutic enzyme, lactate oxidase (LOX) and catalase (CAT), to modulate the tumor microenvironment for the enhanced tumor therapy. The constructed multi-enzyme complex effectively consumed tumor lactate even in the hypoxic conditions, showing the potential usage in tumor treatment which can induce the reprogramming the tumor microenvironment and activation of immune responses against tumors. The approaches we described here may provide new opportunities to construct protein cage nanoparticle-based complex nanostructured materials utilized for various biomedical applications and nanostructured biosensor devicesclos

Development of target-tunable P22 VLP-based delivery nanoplatforms using bacterial superglue

Protein cage nanoparticles are widely used as targeted delivery nanoplatforms, because they have well-defined symmetric architectures, high biocompatibility, and enough plasticity to be modified to produce a range of different functionalities. Targeting peptides and ligands are often incorporated on the surface of protein cage nanoparticles. In this research, we adopted the SpyTag/SpyCatcher protein ligation system to covalently display target-specific affibody molecules on the exterior surface of bacteriophage P22 virus-like particles (VLP) and evaluated their modularity and efficacy of targeted delivery. We genetically introduced the 13 amino acid SpyTag peptide into the C-terminus of the P22 capsid protein to construct a target-tunable nanoplatform. We constructed two different SpyCatcher-fused affibody molecules as targeting ligands, SC-EGFRAfb and SC-HER2Afb, which selectively bind to EGFR and HER2 surface markers, respectively. We produced target-specific P22 VLP-based delivery nanoplatforms for the target cell lines by selectively combining SpyTagged P22 VLP and SC-fused affibody molecules. We confirmed its target-switchable modularity through cell imaging and verified the target-specific drug delivery efficacy of the affibody molecules displaying P22 VLP using cell viability assays. The P22 VLP-based delivery nanoplatforms can be used as multifunctional delivery vehicles by ligating other functional proteins, as well as affibody molecules. The interior cavity of P22 VLP can be also used to load cargoes like enzymes and therapeutic proteins. We anticipate that the nanoplatforms will provide new opportunities for developing target-specific functional protein delivery systems