Jiahn Choi, Ph.D.

Our research centers on understanding how intestinal stem cells and their surrounding niche adapt to environmental stressors—such as aging and diet—and how these adaptations influence tissue homeostasis, inflammation, and cancer risk. Our work integrates single-cell omics, in vivo imaging, and functional genomics to uncover how stem cell plasticity and niche interactions are reprogrammed in response to modifiable risk factors, including a Western-style diet.

We have demonstrated that western-style diet reshapes intestinal homeostasis by altering the primary stem cell population, thereby remodeling lineage differentiation and contributing to a pro-tumorigenic state.

Building on these findings, our ongoing research explores:

• Identifying regulatory mechanisms that drive remodeling of intestinal mucosa in response to environmental stimuli.
• Investigating the impact of aging on the adaptability of the intestinal mucosa following tissue damage.
• Deconvolving the mechanisms by which cellular adaptation contributes to pathogenesis, such as cancer.

By defining the mechanisms underlying mucosal remodeling and pathogenesis, our goal is to develop preventive strategies that preserve epithelial integrity and reduce the risk of diet- and age-associated diseases.

1. MP Verhagen, R Joosten, M Schmitt, N Välimäki, A Sacchetti, K Rajamäki, J Choi, P Procopio, S Silva, B van der Steen, TPP van den Bosch, D Seinstra, AC. de Vries, M Doukas, LH. Augenlicht, LA. Aaltonen, R Fodde, “Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation,” Nature Genetics, 56: 1456 – 1467, 2024
2. J Choi*, LH. Augenlicht, “Intestinal stem cells: guardians of homeostasis in health and aging amid environmental challenges,” Experimental & Molecular Medicine, 1-6, 2024 (*corresponding author).
3. J Choi, X Zhang, W Li, M Houston, K Peregrina, R Dubin, K Ye, LH. Augenlicht, “Dynamic intestinal stem cell plasticity and lineage remodeling by a nutritional environment relevant to human risk for tumorigenesis,” Molecular Cancer Research, 21 (8): 808–824, 2023, editorially selected for highlight and commentary. PMCID: PMC10390890
4. J Choi*, M Houston, R Wang, K Ye, W Li, X Zhang, DM. Huffman, LH. Augenlicht, “Intestinal stem cell aging at single-cell resolution: Transcriptional perturbations alter cell developmental trajectory reversed by gerotherapeutics,” Aging Cell, 22, e13802, 2023 (*corresponding author). PMCID: PMC10186593
5. M Nauman, S Varshney, J Choi, LH. Augenlicht, P Stanley, “EOGT enables residual Notch signaling in mouse intestinal cells lacking Pofut1,” Scientific Reports,13:17473, 2023
6. J Choi, N Rakhilin, P Gadamsetty, DJ Joe, T Tabrizian, SM Lipkin, DM Huffman, X Shen, N Nishimura, “Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging,” Scientific Reports, 8(1):10989, 2018. PMCID: PMC6054609
7. KY Chen, T Srinivasan, KL Tung, JM Belmonte, L Wang, PKL Murthy, J Choi, N Rakhilin, S King, A. K Varanko, M Witherspoon, N Nishimura, JA Glazier, SM Lipkin, P Bu, X Shen, “A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal,” Molecular Systems Biology, 13(4):927, 2017. PMCID: PMC5408779
8. N Rakhilin, B Barth, J Choi, NL Muñoz, S Kulkarni, JS Jones, DM Small, YT Cheng, Y Cao, C LaVinka, E Kan, X Dong, M Spencer, P Pasricha, N Nishimura, X Shen, “Simultaneous optical and electrical in vivo analysis of the enteric nervous system,” Nature Communication, 7:11800, 2016, PMCID: PMC4899629
9. HJ. Chen, J Sun, Z Huang, H Hou, M Arcilla, N Rakhilin, DJ. Joe, J Choi, P Gadamsetty, J Milsom, G Nandakumar, R Longman, XK. Zhou, R Edwards, J Chen, KY Chen, P Bu, L Wang, Y Xu, R Munroe, C Abratte, A Miller, Z Gümüş, M Shuler, N Nishimura, W Edelmann, X Shen, SM Lipkin, “Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting,” Nature Biotechnology, 33(6):656-60, 2015. PMCID: PMC4532544

A complete list of our publications can be found at https://scholar.google.com/citations?hl=en&user=pMtGtAEAAAAJ