Publications

1. Wang D*, Lim S*, van de Wetering WJ, Lopez-Iglesias C, Okura Y, Teranishi-Ikawa Y, Mizoroki A, Spoelstra WK, Dayton T, van Son GJF, Pronk A, Smakman N, Gonera-de Jong GBC, Withoff S, Jonkers IH, van Zon JS, Tans SJ, Peters PJ, van Es JH, Clevers H. “Human gut M cells resemble dendritic cells and present gluten antigen.” Nature 650, 251-260 (2026)

(*denotes co-first author)

2. Willemsen S, Yanti NLWE, van Es JH, Clevers H*, Lim S*. “Protocol for the generation and differentiation of thymic epithelial organoids from adult mouse thymus tissue.” STAR Protocols Vol.6(2) (2025); 103883
(*denotes co-corresponding author)

3. Wijnakker JJAPM, van Son GJF, Krueger D, vdWetering WJ, Lopez-Iglesia C, Schreurs R, vRijt F, Lim S, Lin L, Peters PJ, Isberg RR, Janda CY, Lau W, Clevers H. “Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D

organoid sheets” PNAS (2024) 122(1):e2420595121

4. Mizutani T*, Boretto M*, Lim S, Drost J, Montiel González D, Oka R, Geurts MH, Begthel H, Korving J, van Es JH, van Boxtel R, Clevers H. “Recapitulating the adenoma-carcinoma sequence by selection of four spontaneous oncogenic mutations in mismatch repair-deficient human colon organoids.” Nature Cancer 5(12) (2024):1852-1867

5. Boretto M, Geurts MH, Gandhi S, Ma Z, Staliarova N, Celotti M, Lim S, He GW, Millen R, Driehuis E, Begthel H, Smabers L, Roodhart J, van Es J, Wu W, Clevers H. “Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7.” PNAS 121(12)

(2024):e2309902121

6. Lim S, van Son GJF, Yanti NLWE, Andersson-Rolf A, Willemsen S, Korving J, Lee HG, Begthel H, Clevers H. “Derivation of thymic epithelial organoid lines from adult murine thymus.” Cell Reports Vol.43(4) (2024); 114019

7. Nahon DM*, Moerkens R*, Aydogmus H, Lendemeijer B, Martínez-Silgado A, Stein JM, Dostanić M, Frimat JP, Gontan C, de Graaf MNS, Hu M, Kasi DG, Koch LS, Le KTT, Lim S, Middelkamp HHT, Mooiweer J, Motreuil-Ragot P, Niggl E, Pleguezuelos-Manzano C, Puschhof J, Revyn N, Rivera-Arbelaez JM, Slager J, Windt LM, Zakharova M, van Meer BJ, Orlova VV, de Vrij FMS, Withoff S, Mastrangeli M, van der Meer AD, Mummery CL. “Standardizing designed and emergent quantitative features in microphysiological systems”

Nature Biomedical Engineering (2024) 8(8):941-962

8. Kim GR*, Kim WJ*, Lim S*, Lee HG, Koo JH, Nam KH, Kim SM, Park SD, Choi JM. “In vivo induction of regulatory T cells via CTLA-4 signaling peptide to control autoimmune encephalomyelitis and prevent disease relapse.” Advanced Science Vol.8(14) (2021); 2004973

(*denotes co-first author)

9. Lee HG, Lee JU, Kim DH, Lim S, Kang I, Choi JM. “Pathogenic function of bystanderactivated memory-like CD4+ T cells in autoimmune encephalomyelitis.” Nature Communications (2019) 10(1):709

10. Kim DH, Park HJ, Lim S, Koo JH, Lee HG, Choi JO, Oh JH, Ha SJ, Kang MJ, Lee CM, Lee CG, Elias JA, Choi JM. “Regulation of chitinase-3-like-1 in T cell elicits Th1 and cytotoxic responses to inhibit lung metastasis.” Nature Communications (2018) 9(1):503

11. Lim S, Kirkile-Smith NC, Pober JS, Bothwell ALM, Choi JM. “Regulation of human T cell responses by dNP2-ctCTLA-4 inhibits human skin and microvessel graft rejection.” Biomaterials 183 (2018): 128–138

12. Lim S, Sohn JH, Koo JH, Park JW, Choi JM. “dNP2-ctCTLA-4 inhibits German cockroach extract-induced allergic airway inflammation and hyperresponsiveness via inhibition Th2 responses.” Experimental & Molecular Medicine 49 (2017), e362; doi:10.1038/emm.2017.107

13. Lim S, Lee JA, Koo JH, Kang TG, Ha SJ, Choi JM. “Cell type preference of a novel human derived cell-permeable peptide dNP2 and TAT in murine splenic immune cells.” PLOS One 11 (2016);(5):e0155689. doi:10.1371/journal.pone.0155689

14. Lim S, Koo JH, Choi JM. “Use of cell-penetrating peptides in dendritic cell-based vaccination.” Immune Network 16 (2016);(1):33-43. doi:10.4110/in.2016.16.1.33 15. Lim S*, Kim WJ*, Kim YH, Lee S, Koo JH, Lee JA, Yoon H, Kim DH, Park HJ, Kim HM, Lee HG, Kim JY, Lee JU, Shin JH, Kim LK, Doh J, Kim H, Lee SK, Bothwell ALM, Suh M, Choi JM. “dNP2 is a blood-brain barrier-permeable peptide enabling ctCTLA-4 protein delivery to ameliorate experimental autoimmune encephalomyelitis.” Nature Communications 6 (2015), 8244, doi:10.1038/ncomms9244 (*denotes co-first author)

16. Koo JH, Yoon H, Kim WJ, Lim S, Park HJ, Choi JM. “Cell permeable penetrating function of the nuclear localization sequence in human cytokine IL-1a.” Molecular Biology Reports 41 (2014) 8117-8126

17. Park HJ, Kim DH, Lim S, Kim WJ, Youn J, Choi YS, Choi JM. “Insights into the role of follicular helper T cells in autoimmunity” Immune Network (2014) 14(1):21-29

18. Lim S, Kim WJ, Kim YH, Choi JM. “Identification of a Novel Cell-penetrating peptide from Human Phosphatidate Phosphatase LPIN3.” Molecules and Cells 34 (2012) 577-582