Tiger (Yu Kang) Xu

I am a PhD student and Kavli NDI Distinguished graduate fellow in the Solomon H. Snyder Department of Neuroscience at Johns Hopkins School of Medicine, where I am advised by Dwight Bergles and Jeremias Sulam.

Prior to Johns Hopkins, I obtained my B.Sc. in Physiology at McGill University in Montreal, and completed my honors thesis in the lab of Jack Antel, devising high-throughput drug-screening pipelines to identify therapeutics for multiple sclerosis.

My current research focuses on:

Whole-brain mapping of oligodendrocyte patterns (check out some cool videos and data),
Uncovering the relationship between brain vasculature and oligodendrocyte progenitor cells,
Examining the mechanisms of nodal plasticity in vivo,
Building computational pipelines and deep learning algorithms for cell tracing and tracking,

Outside the lab, I am a casual musician and eager supporter of the performing arts, co-founding a production company, Two Gents of New West, that aims to help young aspiring artists by giving a voice to innovative new stories and projects.

contact: yxu130 at jhmi dot edu

publications

2023
NM

Cross-modality supervised image restoration enables nanoscale tracking of synaptic plasticity in living mice

Xu, Y., Graves, A., Coste, G., Huganir, R., Bergles, D., Charles, A., and Sulam, J.

Abstract

Learning is thought to involve changes in glutamate receptors at synapses, submicron structures that mediate communication between neurons in the central nervous system. Due to their small size and high density, synapses are difficult to resolve in vivo, limiting our ability to directly relate receptor dynamics to animal behavior. Here we developed a combination of computational and biological methods to overcome these challenges. First, we trained a deep-learning image-restoration algorithm that combines the advantages of ex vivo super-resolution and in vivo imaging modalities to overcome limitations specific to each optical system. When applied to in vivo images from transgenic mice expressing fluorescently labeled glutamate receptors, this restoration algorithm super-resolved synapses, enabling the tracking of behavior-associated synaptic plasticity with high spatial resolution. This method demonstrates the capabilities of image enhancement to learn from ex vivo data and imaging techniques to improve in vivo imaging resolution.
2021
Frontiers

Automated in vivo Tracking of Cortical Oligodendrocytes

Xu, Y., Call, C., Sulam, J., and Bergles, D.

Abstract

\textlessp\textgreaterOligodendrocytes exert a profound influence on neural circuits by accelerating action potential conduction, altering excitability, and providing metabolic support. As oligodendrogenesis continues in the adult brain and is essential for myelin repair, uncovering the factors that control their dynamics is necessary to understand the consequences of adaptive myelination and develop new strategies to enhance remyelination in diseases such as multiple sclerosis. Unfortunately, few methods exist for analysis of oligodendrocyte dynamics, and even fewer are suitable for \textlessitalic\textgreaterin vivo\textless/italic\textgreater investigation. Here, we describe the development of a fully automated cell tracking pipeline using convolutional neural networks (\textlessitalic\textgreaterOligo-Track\textless/italic\textgreater) that provides rapid volumetric segmentation and tracking of thousands of cells over weeks \textlessitalic\textgreaterin vivo\textless/italic\textgreater. This system reliably replicated human analysis, outperformed traditional analytic approaches, and extracted injury and repair dynamics at multiple cortical depths, establishing that oligodendrogenesis after cuprizone-mediated demyelination is suppressed in deeper cortical layers. Volumetric data provided by this analysis revealed that oligodendrocyte soma size progressively decreases after their generation, and declines further prior to death, providing a means to predict cell age and eventual cell death from individual time points. This new CNN-based analysis pipeline offers a rapid, robust method to quantitatively analyze oligodendrocyte dynamics \textlessitalic\textgreaterin vivo\textless/italic\textgreater, which will aid in understanding how changes in these myelinating cells influence circuit function and recovery from injury and disease.\textless/p\textgreater
2019
Comms

Deep learning for high-throughput quantification of oligodendrocyte ensheathment at single-cell resolution

Xu, Y., Chitsaz, D., Brown, R., Cui, Q., Dabarno, M., Antel, J., and Kennedy, T.

Abstract

High-throughput quantification of oligodendrocyte myelination is a challenge that, if addressed, would facilitate the development of therapeutics to promote myelin protection and repair. Here, we established a high-throughput method to assess oligodendrocyte ensheathment in-vitro, combining nanofiber culture devices and automated imaging with a heuristic approach that informed the development of a deep learning analytic algorithm. The heuristic approach was developed by modeling general characteristics of oligodendrocyte ensheathments, while the deep learning neural network employed a UNet architecture and a single-cell training method to associate ensheathed segments with individual oligodendrocytes. Reliable extraction of multiple morphological parameters from individual cells, without heuristic approximations, allowed the UNet to match the accuracy of expert-human measurements. The capacity of this technology to perform multi-parametric analyses at the level of individual cells, while reducing manual labor and eliminating human variability, permits the detection of nuanced cellular differences to accelerate the discovery of new insights into oligodendrocyte physiology.
2021
Stem

One-step Reprogramming of Human Fibroblasts into Oligodendrocyte-like Cells by SOX10, OLIG2, and NKX6.2

Chanoumidou, K., Hernández-Rodríguez, B., Windener, F., Thomas, C., Stehling, M., Mozafari, S., Albrecht, S., Ottoboni, L., Antel, J., Kim, K., Velychko, S., Cui, Q., Xu, Y., Martino, G., Winkler, J., Schöler, H., Baron-Van Evercooren, A., Boespflug-Tanguy, O., Vaquerizas, J., Ehrlich, M., and Kuhlmann, T.

Abstract

Limited access to human oligodendrocytes impairs better understanding of oligodendrocyte pathology in myelin diseases. Here, we describe a method to robustly convert human fibroblasts directly into oligodendrocyte-like cells (dc-hiOLs), which allows evaluation of remyelination-promoting compounds and disease modeling. Ectopic expression of SOX10, OLIG2, and NKX6.2 in human fibroblasts results in rapid generation of O4+ cells, which further differentiate into MBP+ mature oligodendrocyte-like cells within 16 days. dc-hiOLs undergo chromatin remodeling to express oligodendrocyte markers, ensheath axons, and nanofibers in vitro, respond to promyelination compound treatment, and recapitulate in vitro oligodendroglial pathologies associated with Pelizaeus-Merzbacher leukodystrophy related to PLP1 mutations. Furthermore, DNA methylome analysis provides evidence that the CpG methylation pattern significantly differs between dc-hiOLs derived from fibroblasts of young and old donors, indicating the maintenance of the source cells’ “age.” In summary, dc-hiOLs represent a reproducible technology that could contribute to personalized medicine in the field of myelin diseases., • SOX10, OLIG2, and NKX6.2 directly convert human fibroblasts into dc-hiOLs in 16 days • dc-hiOLs express key oligodendrocyte markers • dc-hiOLs preserve the epigenetic age of donor cells • dc-hiOLs from PMD patients show maturation deficit and vulnerability to cell death , In this article, Kuhlmann and colleagues show that human fibroblasts can be directly converted into oligodendrocyte-like cells (dc-hiOLs) upon overexpression of SOX10, OLIG2, and NKX6.2. dc-hiOLs undergo chromatin remodeling to activate oligodendrocyte-related genes, perform ensheathment in vitro, and maintain the epigenetic age of donor cells. The applicability of dc-hiOLs in promyelination compound screening and disease-modeling studies is demonstrated.
2020
Acta

Extrinsic immune cell-derived, but not intrinsic oligodendroglial factors contribute to oligodendroglial differentiation block in multiple sclerosis

Starost, L., Lindner, M., Herold, M., Xu, Y., Drexler, H., Heß, K., Ehrlich, M., Ottoboni, L., Ruffini, F., Stehling, M., Röpke, A., Thomas, C., Schöler, H., Antel, J., Winkler, J., Martino, G., Klotz, L., and Kuhlmann, T.

Abstract

Multiple sclerosis (MS) is the most frequent demyelinating disease in young adults and despite significant advances in immunotherapy, disease progression still cannot be prevented. Promotion of remyelination, an endogenous repair mechanism resulting in the formation of new myelin sheaths around demyelinated axons, represents a promising new treatment approach. However, remyelination frequently fails in MS lesions, which can in part be attributed to impaired differentiation of oligodendroglial progenitor cells into mature, myelinating oligodendrocytes. The reasons for impaired oligodendroglial differentiation and defective remyelination in MS are currently unknown. To determine whether intrinsic oligodendroglial factors contribute to impaired remyelination in relapsing–remitting MS (RRMS), we compared induced pluripotent stem cell-derived oligodendrocytes (hiOL) from RRMS patients and controls, among them two monozygous twin pairs discordant for MS. We found that hiOL from RRMS patients and controls were virtually indistinguishable with respect to remyelination-associated functions and proteomic composition. However, while analyzing the effect of extrinsic factors we discovered that supernatants of activated peripheral blood mononuclear cells (PBMCs) significantly inhibit oligodendroglial differentiation. In particular, we identified CD4+ T cells as mediators of impaired oligodendroglial differentiation; at least partly due to interferon-gamma secretion. Additionally, we observed that blocked oligodendroglial differentiation induced by PBMC supernatants could not be restored by application of oligodendroglial differentiation promoting drugs, whereas treatment of PBMCs with the immunomodulatory drug teriflunomide prior to supernatant collection partly rescued oligodendroglial differentiation. In summary, these data indicate that the oligodendroglial differentiation block is not due to intrinsic oligodendroglial factors but rather caused by the inflammatory environment in RRMS lesions which underlines the need for drug screening approaches taking the inflammatory environment into account. Combined, these findings may contribute to the development of new remyelination promoting strategies.
2020
PLOS

Effects of Biotin on survival, ensheathment, and ATP production by oligodendrocyte lineage cells in vitro

Cui, Q., Lin, Y., Xu, Y., Fernandes, M., Rao, V., Kennedy, T., and Antel, J.

Abstract

Mechanisms implicated in disease progression in multiple sclerosis include continued oligodendrocyte (OL)/myelin injury and failure of myelin repair. Underlying causes include metabolic stress with resultant energy deficiency. Biotin is a cofactor for carboxylases involved in ATP production that impact myelin production by promoting fatty acid synthesis. Here, we investigate the effects of high dose Biotin (MD1003) on the functional properties of post-natal rat derived oligodendrocyte progenitor cells (OPCs). A2B5 positive OPCs were assessed using an in vitro injury assay, culturing cells in either DFM (DMEM/F12+N1) or “stress media” (no glucose (NG)-DMEM), with Biotin added over a range from 2.5 to 250 μg/ml, and cell viability determined after 24 hrs. Biotin reduced the increase in OPC cell death in the NG condition. In nanofiber myelination assays, biotin increased the percentage of ensheathing cells, the number of ensheathed segments per cell, and length of ensheathed segments. In dispersed cell culture, Biotin also significantly increased ATP production, assessed using a Seahorse bio-analyzer. For most assays, the positive effects of Biotin were observed at the higher end of the dose-response analysis. We conclude that Biotin, in vitro, protects OL lineage cells from metabolic injury, enhances myelin-like ensheathment, and is associated with increased ATP production.
2020
SciAdv

Multiple sclerosis iPS-derived oligodendroglia conserve their properties to functionally interact with axons and glia in vivo

Mozafari, S., Starost, L., Manot-Saillet, B., Garcia-Diaz, B., Xu, Y., Roussel, D., Levy, M., Ottoboni, L., Kim, K., Schöler, H., Kennedy, T., Antel, J., Martino, G., Angulo, M., Kuhlmann, T., and Baron-Van Evercooren, A.

Abstract

Remyelination failure in multiple sclerosis (MS) is associated with a migration/differentiation block of oligodendroglia. The reason for this block is highly debated. It could result from disease-related extrinsic or intrinsic regulators in oligodendroglial biology. To avoid confounding immune-mediated extrinsic effect, we used an immune-deficient mouse model to compare induced pluripotent stem cell–derived oligodendroglia from MS and healthy donors following engraftment in the developing CNS. We show that the MS-progeny behaves and differentiates into oligodendrocytes to the same extent as controls. They generate equal amounts of myelin, with bona fide nodes of Ranvier, and promote equal restoration of their host slow conduction. MS-progeny expressed oligodendrocyte- and astrocyte-specific connexins and established functional connections with donor and host glia. Thus, MS oligodendroglia, regardless of major immune manipulators, are intrinsically capable of myelination and making functional axo-glia/glia-glia connections, reinforcing the view that the MS oligodendrocyte differentiation block is not from major intrinsic oligodendroglial deficits.
2019
PNAS

pHERV-W envelope protein fuels microglial cell-dependent damage of myelinated axons in multiple sclerosis

Kremer, D., Gruchot, J., Weyers, V., Oldemeier, L., Göttle, P., Healy, L., Ho Jang, J., Kang T. Xu, Y., Volsko, C., Dutta, R., Trapp, B., Perron, H., Hartung, H., and Küry, P.

Abstract

Axonal degeneration is central to clinical disability and disease progression in multiple sclerosis (MS). Myeloid cells such as brain-resident microglia and blood-borne monocytes are thought to be critically involved in this degenerative process. However, the exact underlying mechanisms have still not been clarified. We have previously demonstrated that human endogenous retrovirus type W (HERV-W) negatively affects oligodendroglial precursor cell (OPC) differentiation and remyelination via its envelope protein pathogenic HERV-W (pHERV-W) ENV (formerly MS-associated retrovirus [MSRV]-ENV). In this current study, we investigated whether pHERV-W ENV also plays a role in axonal injury in MS. We found that in MS lesions, pHERV-W ENV is present in myeloid cells associated with axons. Focusing on progressive disease stages, we could then demonstrate that pHERV-W ENV induces a degenerative phenotype in microglial cells, driving them toward a close spatial association with myelinated axons. Moreover, in pHERV-W ENV-stimulated myelinated cocultures, microglia were found to structurally damage myelinated axons. Taken together, our data suggest that pHERV-W ENV-mediated microglial polarization contributes to neurodegeneration in MS. Thus, this analysis provides a neurobiological rationale for a recently completed clinical study in MS patients showing that antibody-mediated neutralization of pHERV-W ENV exerts neuroprotective effects.