Jimmy Lee

Jimmy Lee
Wellcome Sanger Institute · Cellular Genetics

Doctor of Philosophy

About

16
Publications
1,830
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209
Citations
Featured research
Preprint
Full-text available
Single cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single cell data we have developed scfind, a search engine for cell atlases. Using transcriptome data from mouse cell atlases we show how scfind can be used to evaluate marker genes, to perform in silico gating, and to identify both cell-type specific and housekeeping genes. Moreover, we have developed a subquery optimization routine to ensure that long and complex queries return meaningful results. To make scfind more user friendly and accessible, we use indices of PubMed abstracts and techniques from natural language processing to allow for arbitrary queries. Finally, we show how scfind can be used for multi-omics analyses by combining single-cell ATAC-seq data with transcriptome data.
Preprint
Full-text available
The entorhinal cortex consists of several important cell types including, the grid cells, speed cells, border cells and head-direction cells and is important for memory, spatial navigation and perception of time. Here, we trace in detail the development of the entorhinal cortex. Using single-cell profiling we provide unique transcriptional signatures for glia, excitatory and inhibitory neurons existing in the region, including RELN+ cells in layer (L) II and superficial pyramidal neurons. We identified a sandwich layered cortex, where LII emerges prior to LIII and superficial cells maintain a deep layer molecular identity after birth. Our findings contribute to the understanding of the formation of the brains cognitive memory and spatial processing system and provides insight into the transcriptional identity and spatial position of the entorhinal cells.
Article
Full-text available
Aims/hypothesis: Growing evidence supports that dysregulation of adipose tissue-derived factors contributes to the pathogenesis of diabetes and its complications. Since our global gene profiling analysis has identified lipocalin-14 (LCN14)-a secretory protein with lipid-binding properties-as a potential adipokine highly expressed in white adipose tissue (WAT), this study aims to explore the metabolic roles of LCN14 in obese mice, and to investigate the functional mechanisms involved. Methods: Immunoassays and western blotting were performed to determine the circulating level and tissue distribution of LCN14, respectively. Recombinant adeno-associated virus (rAAV)-mediated gene delivery was used to overexpress LCN14 in diet-induced obese (DIO) mice and the effects on glucose and lipid metabolism were examined. Results: LCN14 is expressed predominantly in WAT. Both circulating levels of LCN14 and its expression in adipose tissues are repressed in DIO and genetically inherited diabetic (db/db) mice. Overexpression of LCN14 by rAAV-mediated gene delivery in DIO mice significantly increased insulin sensitivity in major metabolic tissues and ameliorated hyperglycaemia by inhibiting hepatic gluconeogenesis. The reduced hepatic glucose production is attributed to the suppressive effects of LCN14 on the expression of gluconeogenic genes and on glycerol efflux in adipocytes, possibly by reducing the expression of aquaporin-7. Conclusions/interpretation: Reduced LCN14 expression is involved in the pathogenesis of obesity-related metabolic dysregulation. LCN14 exerts its beneficial effects on glucose homeostasis and insulin sensitivity via its actions in both adipocytes and hepatocytes.
Article
Full-text available
Adropin is a highly conserved polypeptide that has been suggested to act as an endocrine factor that plays important roles in metabolic regulation, insulin sensitivity, and endothelial functions. However, in this study, we provide evidence demonstrating that adropin is a plasma membrane protein expressed abundantly in the brain. Using a yeast two-hybrid screening approach, we identified NB-3/Contactin 6, a brain-specific, non-canonical, membrane-tethered Notch1 ligand, as an interaction partner of adropin. Furthermore, this interaction promotes NB3-induced activation of Notch signaling and the expression of Notch target genes. We also generated and characterized adropin knockout mice to explore the role of adropin in vivo. Adropin knockout mice exhibited decreased locomotor activity and impaired motor coordination coupled with defective synapse formation, a phenotype similar to NB-3 knockout mice. Taken together, our data suggest that adropin is a membrane-bound protein that interacts with the brain-specific Notch1 ligand NB3. It regulates physical activity and motor coordination via the NB-3/Notch signaling pathway and plays an important role in cerebellum development in mice.
Article
A widely used concept from machine learning is put to use for single-cell analysis

Publications

Publications (11)
Preprint
Full-text available
Single cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single cell data we have developed scfind, a search engine for cell atlases. Using transcriptome data from mouse cell atlases we show how scfind ca...
Article
A widely used concept from machine learning is put to use for single-cell analysis
Preprint
Full-text available
The entorhinal cortex consists of several important cell types including, the grid cells, speed cells, border cells and head-direction cells and is important for memory, spatial navigation and perception of time. Here, we trace in detail the development of the entorhinal cortex. Using single-cell profiling we provide unique transcriptional signatur...
Article
Full-text available
Aims/hypothesis: Growing evidence supports that dysregulation of adipose tissue-derived factors contributes to the pathogenesis of diabetes and its complications. Since our global gene profiling analysis has identified lipocalin-14 (LCN14)-a secretory protein with lipid-binding properties-as a potential adipokine highly expressed in white adipose...
Article
Full-text available
Adropin is a highly conserved polypeptide that has been suggested to act as an endocrine factor that plays important roles in metabolic regulation, insulin sensitivity, and endothelial functions. However, in this study, we provide evidence demonstrating that adropin is a plasma membrane protein expressed abundantly in the brain. Using a yeast two-h...
Preprint
Recent innovations in droplet-based single-cell RNA-sequencing (scRNA-seq) have provided the technology necessary to investigate biological questions at cellular resolution. With the ability to assay thousands of cells in a single capture, pooling cells from multiple individuals has become a common strategy. Droplets can subsequently be assigned to...
Article
Rationale: Over-nutrition will lead to overexpression of PRMT1 but protein hypomethylation is observed in the liver of obese subjects. The dynamic alteration of the expression and methyltransferase activity of PRMT1 in the progression of fatty liver diseases remains elusive. Methods: We used recombinant adeno-associated virus-mediated gene delivery...
Article
Full-text available
Stochastic gene expression leads to inherent variability in expression outcomes even in isogenic single-celled organisms grown in the same environment. The Drop-Seq technology facilitates transcriptomic studies of individual mammalian cells, and it has had transformative effects on the characterization of cell identity and function based on single-...
Article
Full-text available
Single-cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single-cell data we have developed scfind, a single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker g...
Article
Type 2 cytokines are important signals triggering biogenesis of thermogenic beige adipocytes in white adipose tissue (WAT) during cold acclimation. However, how cold activates type 2 immunity in WAT remains obscure. Here we show that cold-induced type 2 immune responses and beiging in subcutaneous WAT (scWAT) are abrogated in mice with adipose-sele...
Article
Full-text available
Kewu Pan, Zhe Huang, Jimmy Tsz Hang Lee, Chi-Ming Wong State Key Laboratory of Pharmaceutical Biotechnology, Department of Medicine, Shenzhen Institute of Research and Innovation, the University of Hong Kong, Pokfulam, Hong Kong Abstract: The TRAMP complex assists the nuclear exosome to degrade a broad range of ribonucleic acid (RNA) substrates by...
Article
Full-text available
A processing is a tightly regulated and highly complex pathway which includes transcription, splicing, editing, transportation, translation and degradation. It has been well-documented that splicing of RNA polymerase II medicated nascent transcripts occurs co-transcriptionally and is functionally coupled to other RNA processing. Recently, increasin...
Article
Full-text available
Most unwanted RNA transcripts in the nucleus of eukaryotic cells, such as splicing-defective pre-mRNAs and spliced-out introns, are rapidly degraded by the nuclear exosome. In budding yeast, a number of these unwanted RNA transcripts, including spliced-out introns, are first recognized by the nuclear exosome cofactor Trf4/5p-Air1/2p-Mtr4p polyadeny...

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