List of Publications

Meyenberg, M., Hakobyan, A., Papac-Milicevic, N (...) Menche, J., Loizou, JI. (2023). Mutational landscape of intestinal crypt cells after long-term in vivo exposure to high fat diet. Sci Rep. 13(1):13964

Chatzeli, L., Bordeu, I., Han, S (...) Alcolea, MP., Simons, BD. (2023). A cellular hierarchy of Notch and Kras signaling controls cell fate specification in the developing mouse salivary gland. Dev Cell. 58(2):94-109.e6

Belenguer, G., Mastrogiovanni, G., Pacini, C (...) Koo, BK., Huch, M. (2022). RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state. Nat Commun. 13(1):334

Kim, J., Koo, BK., Clevers, H. (2022). Organoid Studies in COVID-19 Research. Int J Stem Cells. 15(1):3-13

Kim, SC., Park, JW., Seo, HY (...) Jeong, SY., Ku, JL. (2022). Multifocal Organoid Capturing of Colon Cancer Reveals Pervasive Intratumoral Heterogenous Drug Responses. Adv Sci (Weinh). 9(5):e2103360

Lee, JH., Kim, S., Han, S (...) Koo, BK., Kim, JK. (2022). p57<sup>Kip2</sup> imposes the reserve stem cell state of gastric chief cells. Cell Stem Cell. 29(5):826-839.e9

Vrij, EJ., Scholte Op Reimer, YS., Fuentes, LR (...) van Blitterswijk, CA., Rivron, NC. (2022). A pendulum of induction between the epiblast and extra-embryonic endoderm supports post-implantation progression. Development. 149(20)

Seidlitz, T., Schmäche, T., Garcίa, F (...) Muñoz, J., Stange, DE. (2022). Sensitivity towards HDAC inhibition is associated with RTK/MAPK pathway activation in gastric cancer. EMBO Mol Med. :e15705

Colozza, G., Park, SY., Koo, BK. (2022). Clone wars: From molecules to cell competition in intestinal stem cell homeostasis and disease. Exp Mol Med.

Teriyapirom, I., Batista-Rocha, AS., Koo, BK. (2021). Genetic engineering in organoids. J Mol Med (Berl). 99(4):555-568

Seidlitz, T., Koo, BK., Stange, DE. (2021). Gastric organoids-an in vitro model system for the study of gastric development and road to personalized medicine. Cell Death Differ. 28(1):68-83

Colozza, G., Koo, BK. (2021). Ub and Dub of RNF43/ZNRF3 in the WNT signalling pathway. EMBO Rep. 22(5):e52970

Koo, BK., Bartfeld, S., Alev, C. (2021). Organoids: ready for the revolution? J Mol Med (Berl). 99(4):441-442

Le Rolle, M., Massa, F., Siggers, P (...) Chaboissier, MC., Chassot, AA. (2021). Arrest of WNT/β-catenin signaling enables the transition from pluripotent to differentiated germ cells in mouse ovaries. Proc Natl Acad Sci U S A. 118(30)

Tsukiyama, T., Koo, BK., Hatakeyama, S. (2021). Post-translational Wnt receptor regulation: Is the fog slowly clearing?: The molecular mechanism of RNF43/ZNRF3 ubiquitin ligases is not yet fully elucidated and still controversial. Bioessays. 43(4):e2000297

Yum, MK., Han, S., Fink, J (...) Koo, BK., Simons, BD. (2021). Tracing oncogene-driven remodelling of the intestinal stem cell niche. Nature. 594(7863):442-447

Moon, S., Park, Y., Hyeon, S (...) Ha, SJ., Lee, SW. (2021). Niche-specific MHC II and PD-L1 regulate CD4+CD8αα+ intraepithelial lymphocyte differentiation. J Exp Med. 218(4)

Lu, C., Lin, X., Yamashita, J (...) Matsumoto, I., Jiang, P. (2021). RNF43/ZNRF3 negatively regulates taste tissue homeostasis and positively regulates dorsal lingual epithelial tissue homeostasis. Stem Cell Reports.

Colozza, G., Koo, BK. (2021). Wnt/β-catenin signaling: Structure, assembly and endocytosis of the signalosome. Dev Growth Differ. 63(3):199-218

Seidlitz, T., Koo, BK., Stange, DE. (2021). Correction: Gastric organoids-an in vitro model system for the study of gastric development and road to personalized medicine. Cell Death Differ.

Choi, J., Jang, YJ., Dabrowska, C (...) Kim, J., Lee, JH. (2021). Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. Nat Cell Biol.

Koo, BK. (2021). Methods in organoids: a model that goes beyond our imagination. Exp Mol Med.

Hosmillo, M., Chaudhry, Y., Nayak, K (...) Zilbauer, M., Goodfellow, I. (2020). Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses. mBio. 11(2)

Kim, J., Koo, BK., Knoblich, JA. (2020). Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol. 21(10):571-584

Morkmued, S., Clauss, F., Schuhbaur, B (...) Bloch-Zupan, A., Niederreither, K. (2020). Deficiency of the SMOC2 matricellular protein impairs bone healing and produces age-dependent bone loss. Sci Rep. 10(1):14817

Spit, M., Fenderico, N., Jordens, I (...) Vermeulen, M., Maurice, MM. (2020). RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer. EMBO J. 39(18):e103932

Choi, J., Park, JE., Tsagkogeorga, G (...) Han, N., Lee, JH. (2020). Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration. Cell Stem Cell. 27(3):366-382.e7

Steinway, SN., Saleh, J., Koo, BK., Delacour, D., Kim, DH. (2020). Human Microphysiological Models of Intestinal Tissue and Gut Microbiome. Front Bioeng Biotechnol. 8:725

Tsukiyama, T., Zou, J., Kim, J (...) Koo, BK., Hatakeyama, S. (2020). A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis. Nat Commun. 11(1):4586

Kim, J., Koo, BK., Yoon, KJ. (2019). Modeling Host-Virus Interactions in Viral Infectious Diseases Using Stem-Cell-Derived Systems and CRISPR/Cas9 Technology. Viruses. 11(2)

Seidlitz, T., Chen, YT., Uhlemann, H (...) Koo, BK., Stange, DE. (2019). Mouse Models of Human Gastric Cancer Subtypes With Stomach-Specific CreERT2-Mediated Pathway Alterations. Gastroenterology. 157(6):1599-1614.e2

Basham, KJ., Rodriguez, S., Turcu, AF (...) Val, P., Hammer, GD. (2019). A ZNRF3-dependent Wnt/β-catenin signaling gradient is required for adrenal homeostasis. Genes Dev. 33(3-4):209-220

Wu, SS., Lee, JH., Koo, BK. (2019). Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging. Mol Cells. 42(2):104-112

Seidlitz, T., Merker, SR., Rothe, A (...) Weitz, J., Stange, DE. (2019). Human gastric cancer modelling using organoids. Gut. 68(2):207-217

Kraiczy, J., Nayak, KM., Howell, KJ (...) Koo, BK., Zilbauer, M. (2019). DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Gut. 68(1):49-61

Han, S., Fink, J., Jörg, DJ (...) Simons, BD., Koo, BK. (2019). Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells. Cell Stem Cell. 25(3):342-356.e7

Kashfi, SMH., Almozyan, S., Jinks, N., Koo, BK., Nateri, AS. (2018). Morphological alterations of cultured human colorectal matched tumour and healthy organoids. Oncotarget. 9(12):10572-10584

Spit, M., Koo, BK., Maurice, MM. (2018). Tales from the crypt: intestinal niche signals in tissue renewal, plasticity and cancer. Open Biol. 8(9)

Bollen, Y., Post, J., Koo, BK., Snippert, HJG. (2018). How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing. Nucleic Acids Res. 46(13):6435-6454

Harris, A., Siggers, P., Corrochano, S (...) McElreavey, K., Greenfield, A. (2018). ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling. Proc Natl Acad Sci U S A. 115(21):5474-5479

Koo, BK. (2018). Generation of FLIP and FLIP-FlpE Targeting Vectors for Biallelic Conditional and Reversible Gene Knockouts in Mouse and Human Cells. Methods Mol Biol. 1842:255-264

Nanki, K., Toshimitsu, K., Takano, A (...) Kanai, T., Sato, T. (2018). Divergent Routes toward Wnt and R-spondin Niche Independency during Human Gastric Carcinogenesis. Cell. 174(4):856-869.e17

Howell, KJ., Kraiczy, J., Nayak, KM (...) Stegle, O., Zilbauer, M. (2018). DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome. Gastroenterology. 154(3):585-598

Bartfeld, S., Koo, BK. (2017). Adult gastric stem cells and their niches. Wiley Interdiscip Rev Dev Biol. 6(2)

Andersson-Rolf, A., Zilbauer, M., Koo, BK., Clevers, H. (2017). Stem Cells in Repair of Gastrointestinal Epithelia. Physiology (Bethesda). 32(4):278-289

Merenda, A., Andersson-Rolf, A., Mustata, RC (...) Kim, H., Koo, BK. (2017). A Protocol for Multiple Gene Knockout in Mouse Small Intestinal Organoids Using a CRISPR-concatemer. J Vis Exp. (125)

Andersson-Rolf, A., Mustata, RC., Merenda, A (...) Skarnes, WC., Koo, BK. (2017). One-step generation of conditional and reversible gene knockouts. Nat Methods. 14(3):287-289

Broutier, L., Mastrogiovanni, G., Verstegen, MM (...) van der Laan, LJ., Huch, M. (2017). Human primary liver cancer-derived organoid cultures for disease modeling and drug screening. Nat Med. 23(12):1424-1435

Turco, MY., Gardner, L., Hughes, J (...) Moffett, A., Burton, GJ. (2017). Long-term, hormone-responsive organoid cultures of human endometrium in a chemically defined medium. Nat Cell Biol. 19(5):568-577

Koo, BK., Huch, M. (2016). Organoids: A new in vitro model system for biomedical science and disease modelling and promising source for cell-based transplantation. Dev Biol. 420(2):197-198

Andersson-Rolf, A., Merenda, A., Mustata, RC (...) Dietmann, S., Koo, BK. (2016). Simultaneous paralogue knockout using a CRISPR-concatemer in mouse small intestinal organoids. Dev Biol. 420(2):271-277

Fink, J., Koo, BK. (2016). Clonal Evolution of Stem Cells in the Gastrointestinal Tract. Adv Exp Med Biol. 908:11-25

Broutier, L., Andersson-Rolf, A., Hindley, CJ (...) Koo, BK., Huch, M. (2016). Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation. Nat Protoc. 11(9):1724-43

Andersson-Rolf A, Mustata RC, Merenda A, Perera S, Grego T, Kim J, Andrews K, Fink J, Skarnes WC, Koo BK. (2016). Rapid, one-step generation of biallelic conditional gene knockouts. BioRxiv.

Huch, M., Koo, BK. (2015). Modeling mouse and human development using organoid cultures. Development. 142(18):3113-25

Fink, J., Andersson-Rolf, A., Koo, BK. (2015). Adult stem cell lineage tracing and deep tissue imaging. BMB Rep. 48(12):655-67

Andersson-Rolf A, Koo BK (2015). Stem cell-derived organoid cultures and genome editing tools. Cell Gene Therapy Insights. 1(2):243-251

Schuijers, J., Junker, JP., Mokry, M (...) van Oudenaarden, A., Clevers, H. (2015). Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts. Cell Stem Cell. 16(2):158-70

Koo, BK., van Es, JH., van den Born, M., Clevers, H. (2015). Porcupine inhibitor suppresses paracrine Wnt-driven growth of Rnf43;Znrf3-mutant neoplasia. Proc Natl Acad Sci U S A. 112(24):7548-50

Andersson-Rolf, A., Fink, J., Mustata, RC., Koo, BK. (2014). A video protocol of retroviral infection in primary intestinal organoid culture. J Vis Exp. (90):e51765

Koo, BK., Clevers, H. (2014). Stem cells marked by the R-spondin receptor LGR5. Gastroenterology. 147(2):289-302

Schwank, G., Koo, BK., Sasselli, V (...) Beekman, JM., Clevers, H. (2013). Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell. 13(6):653-8

Koo, BK., Sasselli, V., Clevers, H. (2013). Retroviral gene expression control in primary organoid cultures. Curr Protoc Stem Cell Biol. 27:Unit 5A.6.

Stange, DE., Koo, BK., Huch, M (...) Mills, JC., Clevers, H. (2013). Differentiated Troy+ chief cells act as reserve stem cells to generate all lineages of the stomach epithelium. Cell. 155(2):357-68

Schwank, G., Andersson-Rolf, A., Koo, BK., Sasaki, N., Clevers, H. (2013). Generation of BAC transgenic epithelial organoids. PLoS One. 8(10):e76871

Heijmans, J., van Lidth de Jeude, JF., Koo, BK (...) Muncan, V., van den Brink, GR. (2013). ER stress causes rapid loss of intestinal epithelial stemness through activation of the unfolded protein response. Cell Rep. 3(4):1128-39

Muñoz, J., Stange, DE., Schepers, AG (...) Heck, AJ., Clevers, H. (2012). The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J. 31(14):3079-91

Kim, HA., Koo, BK., Cho, JH (...) Hwang, D., Kong, YY. (2012). Notch1 counteracts WNT/β-catenin signaling through chromatin modification in colorectal cancer. J Clin Invest. 122(9):3248-59

van Es, JH., Haegebarth, A., Kujala, P (...) Robine, S., Clevers, H. (2012). A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal. Mol Cell Biol. 32(10):1918-27

Koo, BK., Spit, M., Jordens, I (...) Maurice, MM., Clevers, H. (2012). Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors. Nature. 488(7413):665-9

Koo, BK., Stange, DE., Sato, T (...) van Es, JH., Clevers, H. (2011). Controlled gene expression in primary Lgr5 organoid cultures. Nat Methods. 9(1):81-3

de Lau, W., Barker, N., Low, TY (...) Heck, AJ., Clevers, H. (2011). Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature. 476(7360):293-7

Kim, NS., Kim, HT., Kwon, MC (...) Cho, Y., Kong, YY. (2011). Survival and differentiation of mammary epithelial cells in mammary gland development require nuclear retention of Id2 due to RANK signaling. Mol Cell Biol. 31(23):4775-88

Min, JK., Park, H., Choi, HJ (...) Hwang, KC., Kwon, YG. (2011). The WNT antagonist Dickkopf2 promotes angiogenesis in rodent and human endothelial cells. J Clin Invest. 121(5):1882-93

Stange, DE., Engel, F., Longerich, T (...) Weitz, J., Radlwimmer, B. (2010). Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain. Gut. 59(9):1236-44

Jeong, HW., Jeon, US., Koo, BK (...) Kim, J., Kong, YY. (2009). Inactivation of Notch signaling in the renal collecting duct causes nephrogenic diabetes insipidus in mice. J Clin Invest. 119(11):3290-300

Kwon, MC., Koo, BK., Kim, YY (...) Kim, JH., Kong, YY. (2009). Essential role of CR6-interacting factor 1 (Crif1) in E74-like factor 3 (ELF3)-mediated intestinal development. J Biol Chem. 284(48):33634-41

Koo, BK., Lim, HS., Chang, HJ (...) Park, JG., Kong, YY. (2009). Notch signaling promotes the generation of EphrinB1-positive intestinal epithelial cells. Gastroenterology. 137(1):145-55, 155.e1-3

Yoon, KJ., Koo, BK., Im, SK (...) Miyata, T., Kong, YY. (2008). Mind bomb 1-expressing intermediate progenitors generate notch signaling to maintain radial glial cells. Neuron. 58(4):519-31

Lee, JH., Kim, TS., Yang, TH (...) Kim, JM., Lim, DS. (2008). A crucial role of WW45 in developing epithelial tissues in the mouse. EMBO J. 27(8):1231-42

Kim, YW., Koo, BK., Jeong, HW (...) Kim, SH., Kong, YY. (2008). Defective Notch activation in microenvironment leads to myeloproliferative disease. Blood. 112(12):4628-38

Song, R., Kim, YW., Koo, BK (...) Yoon, K., Kong, YY. (2008). Mind bomb 1 in the lymphopoietic niches is essential for T and marginal zone B cell development. J Exp Med. 205(11):2525-36

Yoon, MJ., Koo, BK., Song, R (...) Kong, YY., Suh, PG. (2008). Mind bomb-1 is essential for intraembryonic hematopoiesis in the aortic endothelium and the subaortic patches. Mol Cell Biol. 28(15):4794-804

Kwon, MC., Koo, BK., Moon, JS (...) Shong, M., Kong, YY. (2008). Crif1 is a novel transcriptional coactivator of STAT3. EMBO J. 27(4):642-53

Koo, BK., Yoon, MJ., Yoon, KJ (...) Jan, YN., Kong, YY. (2007). An obligatory role of mind bomb-1 in notch signaling of mammalian development. PLoS One. 2(11):e1221

Kim, NS., Kim, HJ., Koo, BK (...) Penninger, JM., Kong, YY. (2006). Receptor activator of NF-kappaB ligand regulates the proliferation of mammary epithelial cells via Id2. Mol Cell Biol. 26(3):1002-13

Yoo, KW., Kim, EH., Jung, SH (...) Kong, YY., Kim, CH. (2006). Snx5, as a Mind bomb-binding protein, is expressed in hematopoietic and endothelial precursor cells in zebrafish. FEBS Lett. 580(18):4409-16

Song, R., Koo, BK., Yoon, KJ (...) Kim, CH., Kong, YY. (2006). Neuralized-2 regulates a Notch ligand in cooperation with Mind bomb-1. J Biol Chem. 281(47):36391-400

Koo, BK., Yoon, KJ., Yoo, KW (...) Kim, CH., Kong, YY. (2005). Mind bomb-2 is an E3 ligase for Notch ligand. J Biol Chem. 280(23):22335-42

Koo, BK., Lim, HS., Song, R (...) Kim, CH., Kong, YY. (2005). Mind bomb 1 is essential for generating functional Notch ligands to activate Notch. Development. 132(15):3459-70