Xiaozhe Ding

• BSc
• PhD Student at California Institute of Technology

A mechanistic understanding of neural computation requires determining how information is processed as it passes through neurons and across synapses. However, it has been challenging to measure membrane potential changes in axons and dendrites in vivo. We use in vivo, two-photon imaging of novel genetically encoded voltage indicators, as well as ca...

Histone modification patterns and their combinatorial readout have emerged as a fundamental mechanism for epigenetic regulation. Here we characterized Spindlin1 as a histone effector that senses a cis-tail histone H3 methylation pattern involving trimethyllysine 4 (H3K4me3) and asymmetric dimethylarginine 8 (H3R8me2a) marks. Spindlin1 consists of t...

Significance Critical for regulating cell function, integral membrane proteins (MPs) are key engineering targets. MP engineering is limited because these proteins are difficult to express with proper plasma membrane localization in heterologous systems. We investigate the expression, localization, and light-induced behavior of the light-gated MP ch...

In vivo protein labelling with a peptide tag–fluorescent probe system is an important chemical biology strategy for studying protein distribution, interaction and function. A variety of engineered tags have been developed to label proteins of interest (POIs), in which a protein or peptide tag is covalently linked to the POIs that can afford fluores...

Protein-protein interactions (PPIs) play a critical role in many essential biological processes, and numerous diseases result from malfunctioning PPIs. The modulation of undesirable PPIs via synthetic chemical molecules has long been considered of medical importance, but still remains challenging. Thanks to the development of synthetic chemistry, c...

Many neurodegenerative diseases feature abnormal protein aggregation in neurons. A notable example is α-synuclein (αSyn) aggregates in Parkinson′s disease (PD). The mechanisms underlying aggregates formation and their contribution to the pathogenesis remain unclear. Here we tackle this question from a build-to-understand perspective by recreating α...

Adeno-associated viruses (AAVs) are foundational gene delivery tools for basic science and clinical therapeutics. However, lack of mechanistic insight, especially for engineered vectors created by directed evolution, can hamper their application. Here, we adapt an unbiased human cell microarray platform to determine the extracellular and cell surfa...

Aim: We present multi-wavelength (MW) analytical ultracentrifugation (AUC) methods offering superior accuracy for adeno-associated virus characterization and quantification. Methods: Experimental design guidelines are presented for MW sedimentation velocity and analytical buoyant density equilibrium AUC. Results: Our results were compared with dual...

Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice...

The blood-brain barrier (BBB) presents a major challenge for delivering large molecules to study and treat the central nervous system. This is due in part to the scarcity of targets known to mediate BBB crossing. To identify novel targets, we leverage a panel of adeno-associated viruses (AAVs) previously identified through mechanism-agnostic direct...

Deep learning-based methods for protein structure prediction have achieved unprecedented accuracy. However, the power of these tools to guide the engineering of protein-based therapeutics remains limited due to a gap between the ability to predict the structures of candidate proteins and the ability to assess which of those proteins are most likely...

Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice...

The blood-brain barrier (BBB) presents a major challenge to delivering large molecules to study and treat the central nervous system (CNS). This is due in part to the scarcity of effective targets for BBB crossing, the identification of which is the crucial first step of drug development. Here, we leveraged a panel of adeno-associated viruses (AAVs...

Adeno-associated virus serotype 9 (AAV9) is a promising gene therapy vector for treating neurodegenerative diseases due to its ability to penetrate the blood-brain barrier. PHP.eB was engineered from AAV9 by insertion of a 7-amino-acid peptide and point mutation of neighboring residues, thereby enhancing potency in the central nervous system. Here...

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension t...

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension t...

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension t...

The neurovascular unit (NVU) is a vital yet understudied component of the nervous system. Malfunction of non-neuronal cell types within the NVU, including endothelial cells, can facilitate the progression of neurological disorders (Yu et al, Frontiers in Neuroscience, 2020), but limited options for cell-type specific transgene delivery hamper its s...

Adeno-associated viruses (AAVs) are typically single-stranded deoxyribonucleic acid (ssDNA) encapsulated within 25-nm protein capsids. Recently, tissue-specific AAV capsids (e.g. PHP.eB) have been shown to enhance brain delivery in rodents via the LY6A receptor on brain endothelial cells. Here, we create a non-invasive positron emission tomography...

The application of recombinant Adeno-Associated Virus (rAAV) vectors as gene delivery vehicles has been limited by the modest packaging capacity (5.2kb) of rAAV. Th is limitation is imposed by the capsid size of 25nm diameter, which is determined by the capsid’s T=1 icosahedral geometry. Current methods for rAAV delivery of oversized cargo, typical...

Adeno-associated viruses (AAVs) are widely used gene delivery vectors due to their ability to transduce dividing and non-dividing cells, their long-term persistence, and low immunogenicity. However, natural AAV serotypes have a limited set of tropisms. Directed evolution has been used to engineer recombinant AAVs to target specific cell types and t...

Recombinant adeno-associated viral (rAAV) capsids are increasingly used as gene delivery vectors in science and in therapeutics. However, there is room for further improvement on the efficiency and specificity to transduce the central nervous system (CNS) via non-invasive systemic delivery. We have shown in the past that marked improvement is possi...

Recombinant adeno-associated viruses (rAAVs) are efficient gene delivery vectors via intravenous delivery; however, natural serotypes display a finite set of tropisms. To expand their utility, we evolved AAV capsids to efficiently transduce specific cell types in adult mouse brains. Building upon our Cre-recombination-based AAV targeted evolution (...

Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanopart...

Recombinant adeno-associated viral (rAAV) capsids are widely accepted as safe gene delivery vehicles in research laboratories and in gene therapy clinical trials and there is potential to further improve their usage by evolving the surface of the capsids to enhance their affinity to specific cell-types or tissues after intravenous (IV) delivery. To...

Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanopart...

Integral membrane proteins (MPs) are key engineering targets due to their critical roles in regulating cell function. In engineering MPs, it can be extremely challenging to retain membrane localization capability while changing other desired properties. We have used structure-guided SCHEMA recombination to create a large set of functionally diverse...

Besides functioning as an electron transporter in the mitochondrial electron transport chain, cytochrome c (cyt c) is also one of the determinants in the execution of cell death. The interaction between cyt c and lipids has long been of great interest in biological systems, while the study of cyt c has attracted even more attention since its new fu...