TaejoonLab

Disease Genes in Xenopus Development

Mon, 01 Jan 0001 00:00:00 +0000

Many genes associated with human disease act first during embryonic development. The African clawed frogs Xenopus laevis and X. tropicalis let us manipulate these genes quickly in large numbers of externally developing embryos, and follow the consequences in cells, tissues, and organs as they form.

Genomic resources

We have contributed to the Xenopus genome assemblies and comparative frog genomics, and to community resources such as Xenbase and the Alliance of Genome Resources, so that disease genes can be studied in the context of the frog genome.

Single-Cell Approaches to Spine and Joint Repair

Mon, 01 Jan 0001 00:00:00 +0000

Injuries to the spine and joints heal poorly because the cells that should rebuild cartilage and other tissues rarely return to a regenerative state. We use single-cell genomics to follow how individual cells change their identity during development, injury, and repair, and to find ways to steer them toward regeneration.

What we study

Single-cell maps of cell fate. Our time-resolved single-cell profiling of the Xenopus mucociliary epithelium showed that cell types can arise through non-hierarchical, convergent routes. We apply the same approach to injured and regenerating tissue.
Cartilage and joint biology. With collaborators we have shown how chondrocytes maintain cartilage, for example through ER-associated degradation and integrin regulation by ITGBL1, which protects against arthritis.
Chondrocyte blastema formation. We study how chondrocytes form a regenerative blastema after injury, as a basis for spine and joint repair.

Selected publications

Leading studies

Chae S#, Park TJ, Kwon T*. (2023) Convergent differentiation of multiciliated cells. , Sci Rep., 13(1):23028. PMID:38155158 doi:10.1038/s41598-023-50077-5.

Collaborative works

Lee J, Møller AF, Chae S, Bussek A, Park TJ, Kim Y, Lee HS, Pers TH, Kwon T, Sedzinski J, Natarajan KN. (2023) A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals nonhierarchical model of development. , Sci Adv., 9(14):eadd5745. PMID:37027470 doi:10.1126/sciadv.add5745.
Sim HJ, Cho C, Kim HE, Hong JY, Song EK, Kwon KY, Jang DG, Kim SJ, Lee HS, Lee C, Kwon T, Yang S*, Park TJ* (2022) Augmented ERAD (ER-associated degradation) activity in chondrocytes is necessary for cartilage development and maintenance , Sci Adv., 8(3):eabl4222 PMID:35061535 doi:10.1126/sciadv.abl4222
Kakebeen AD, Huebner RJ, Shindo A, Kwon K, Kwon T, Wills AE, Wallingford JB (2021) A temporally resolved transcriptome for developing "Keller" explants of the Xenopus laevis dorsal marginal zone , Dev. Dyn., 250(5):717-731 PMID:33368695 doi:10.1002/dvdy.289
Song EK, Jeon J, Jang DG, Kim HE, Sim HJ, Kwon KY, Medina-Ruiz S, Jang HJ, Lee AR, Rho JG, Lee HS, Kim SJ, Park CY, Myung K, Kim W, Kwon T, Yang S, Park TJ (2018) ITGBL1 modulates integrin activity to promote cartilage formation and protect against arthritis , Sci Transl Med., PMID:30305454 doi:10.1126/scitranslmed.aam7486

CRISPR-Based Cancer Therapeutics

Mon, 01 Jan 0001 00:00:00 +0000

Cancer genomes carry mutations that normal cells do not. We use these differences as targets: CRISPR nucleases guided to cancer-specific sequences can cut and kill cancer cells while sparing normal cells.

What we study

Targeting cancer-specific mutations. We showed that CRISPR-Cas9 guided to cancer-specific insertion/deletion (InDel) mutations can precisely eliminate tumor cells. Multiplexed Cas9 nickases combined with PARP inhibitors make this strategy more efficient and precise.
Cancer genomics and DNA damage. Genome analysis of patient-derived tumor models and studies of the DNA damage response identify vulnerabilities to target.
Cell state and cell death. Single-cell phenotyping of how cells respond to damage and undergo cell death.
Patient-derived models. Bioprinted patient-derived organoids and tissue-derived matrices let us test therapies in models that capture features of each patient’s tumor.

Selected publications

Leading studies

Jeong H#, Moon HE, Yun S, Cho SW, Park HR, Park SH, Myung K, Kwon T*, Paek SH*. (2023) Enrichment of Deleterious Mutated Genes Involved in Ciliary Function and Histone Modification in Brain Cancer Patient-Derived Xenograft Models. , Biomedicines., 11(11):2934. PMID:38001935 doi:10.3390/biomedicines11112934.
Jeong H#, Wie M#, Baek IJ, Sohn G, Um SH, Lee SG, Seo Y, Ra J, Lee EA, Kim S, Kim BG, Deshpande RA, Paull TT, Han JS, Kwon T*, Myung K*. (2022) TRIP13 Participates in Immediate-Early Sensing of DNA Strand Breaks and ATM Signaling Amplification through MRE11. , Cells, 11(24):4095 PMID:36552858 doi:10.3390/cells11244095
Kwon T#*, Ra JS#, Lee S#, Baek I-J#, Khim KW, Lee EA, Song EK, Otarbayev D, Jung W, Park YH, Wie M, Bae J, Cheng H, Park JH, Kim N, Seo Y, Yun S, Kim HE, Moon HE, Paek SH, Park TJ, Park YU, Rhee H, Choi JH, Cho SW*, Myung K* (2022) Precision targeting tumor cells using cancer-specific InDel mutations with CRISPR-Cas9 , Proc Natl Acad Sci USA, 19(9):e2103532119 PMID:35217600 doi:10.1073/pnas.2103532119

Collaborative works

Yoon H, Kim D, Jeong HJ, Han H, Kim SJ, Jang J, Jung DB, Myung SJ, Yu CS, Song IH, Choi JH, Corces MR, Kwon T, Myung K, Joo J, Kang JH, Park TE, Cho SW. (2026) Tissue-derived extracellular matrix hydrogels instruct epigenetic adaptation in metastatic colonization. , Bioact Mater., 67:757-773. PMID:42699228 doi:10.1016/j.bioactmat.2026.08.031
Lee S, Kim K, Jeong HJ, Choi S, Cheng H, Kim D, Heo S, Mun J, Kim M, Lee E, Choi YJ, Lee SG, Lee EA, Jang Y, Lim K, Kim HS, Jeong E, Myung SJ, Jung DB, Yu CS, Song IH, Corces MR, Kang JH, Myung K, Kwon T, Park TE, Joo J, Cho SW. (2025) Combining Multiplexed CRISPR/Cas9-Nickase and PARP Inhibitors Efficiently and Precisely Targets Cancer Cells. , Cancer Res., 85(15):2890-2904. PMID:40327605 doi:10.1158/0008-5472.CAN-24-2938
Han J, Jeong HJ, Choi J, Kim H, Kwon T, Myung K, Park K, Park JI, Sánchez S, Jung DB, Yu CS, Song IH, Shim JH, Myung SJ, Kang HW, Park TE. (2025) Bioprinted Patient-Derived Organoid Arrays Capture Intrinsic and Extrinsic Tumor Features for Advanced Personalized Medicine. , Adv Sci (Weinh)., 12(20):e2407871. PMID:40151904 doi:10.1002/advs.202407871
Hong J, Kwon KY, Jang DG, Kwon T, Yoon H, Park TJ. (2024) Mebendazole preferentially inhibits cilia formation and exerts anticancer activity by synergistically augmenting DNA damage. , Biomed Pharmacother., 174:116434. PMID:38513592 doi:10.1016/j.biopha.2024.116434.

Imaging-Based Phenomics and Genomics for Diagnosis

Mon, 01 Jan 0001 00:00:00 +0000

Linking genes to disease needs phenotypes that can be measured at scale, and diagnosis needs genomic information that can be read quickly and accurately. We develop imaging-based phenotyping and genome analysis for both.

What we study

Imaging-based phenomics. Automated imaging of Xenopus embryos and tissues to score phenotypes in disease models and chemical screens, for example to identify agents that act on the mucociliary epithelium.
Microbial diagnostics. Genome-informed probes and assays for fast identification of pathogenic bacteria, including FRET-based peptide nucleic acid probes and quantitative FISH of magnetically captured bacteria for early detection of infection.
Microbial genomics. Analysis of the blood microbiome and of bacterial genome evolution and antibiotic resistance, building on our long-term work on Pseudomonas aeruginosa.
Molecular measurement methods. Proteomics and transcriptomics methods, such as characterizing the ciliary proteome, that make phenotypes measurable at the molecular level.

Selected publications

Leading studies

Kim S#, Hyun H#, Im JK, Lee MS, Koh H, Kang D, Nho SH, Kang JH*, Kwon T*, Kim H*. (2024) Fast and accurate multi-bacterial identification using cleavable and FRET-based peptide nucleic acid probes. , Biosens Bioelectron., 271:116950. PMID:39631211 doi:10.1016/j.bios.2024.116950.
Lee MS#, Hyun H#, Park I#, Kim S#, Jang D-H, Kim S, Im J-K, Kim H*, Lee JH*, Kwon T*, and Kang JH* (2022) Quantitative fluorescence in situ hybridization (FISH) of magnetically confined bacteria enables early detection of human bacteremia , Small Methods, e2101239 PMID:35112812 doi:10.1002/smtd.202101239
Hyun H#, Lee MS#, Park I#, Ko HS, Yun S, Jang DH, Kim S, Kim H, Kang JH*, Lee JH*, Kwon T** (2021) Analysis of Porcine Model of Fecal-Induced Peritonitis Reveals the Tropism of Blood Microbiome , Front. Cell. Infect. Microbiol., 11:676650 PMID:34527598 doi:10.3389/fcimb.2021.676650
Yang HS#, Sim HJ#, Cho H, Bang WY, Kim HE, Kwon TK, Kwon T*, Park TJ* (2020) Alpha-tocopherol exerts protective function against the mucotoxicity of particulate matter in amphibian and human goblet cells , Sci Rep., 10(1):6224 PMID:32277121 doi:10.1038/s41598-020-63085-6
Sim HJ#, Yun S#, Kim HE, Kwon KY, Kim GH, Yun S, Kim BG, Myung K, Park TJ*, Kwon T* (2020) Simple Method To Characterize the Ciliary Proteome of Multiciliated Cells, J Proteome Res., 19(1):391-400 PMID:31689115 doi:10.1021/acs.jproteome.9b00589
Huse HK#, Kwon T#, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M (2010) Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo , mBio, 1(4):e00199-10 PMID:20856824 doi:10.1128/mBio.00199-10

Collaborative works

Sim HJ, Kim SH, Myung KJ, Kwon T, Lee HS, Park TJ (2018) Xenopus: An alternative model system for identifying muco-active agents , PLoS ONE, PMID:29470529 doi:10.1371/journal.pone.019331
Murray JL, Kwon T, Marcotte EM, Whiteley M (2015) Intrinsic antimicrobial resistance determinants In the superbug Pseudomonas aeruginosa , mBio, 6(6):e01603-15 PMID:26507235 doi:10.1128/mBio.01603-15

Members

Wed, 18 Jan 2023 00:00:00 +0000

Publications before TaejoonLab

Tue, 17 Jan 2023 00:00:00 +0000

About Us

Mon, 01 Jan 0001 00:00:00 +0000

Affiliations

Location

울산광역시 울주군 유니스트길 50 울산과학기술원 110동(EB4) 705호 우. 44919
Building 110 (EB4) Room 705, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulju-gun, Ulsan, 44919, Republic of Korea

Photos

Mon, 01 Jan 0001 00:00:00 +0000