Publications

Featured publications

Modelling hepatoblastoma using organoids

doi: https://www.nature.com/articles/s41467-024-52757-w

Kluiver TA#, Lu Y#, Schubert SA, Kraaier LJ, Ringnalda F, Lijnzaad P, DeMartino J, Megchelenbrink WL, Amo-Addae V, Eising S, de Faria FW, Münter DJ, van de Wetering M, Kerl K, Duiker E, van den Heuvel M, de Meijer VE, de Kleine RH, de Krijger RR, Molenaar JJ, Margaritis T, Stunnenberg H, Zsiros J, Clevers H, Peng WC*. Divergent WNT Signaling and Drug Sensitivity Profiles within Hepatoblastoma Tumors and Organoids. Nat Commun.2024; 15, 8576.

WNT-activating mutations in CTNNB1 are common in hepatoblastoma, but downstream molecular phenotypes are heterogenous. Using multiomic approaches, we identify distinct subgroups of hepatoblastoma cells based on WNT-signaling patterns. These tumor subtypes are distinguished by staining of the transcription factors HNF4A and LEF1. We create a biobank of patient-derived hepatoblastoma organoids representing these different subtypes and demonstrate their sensitivity to HDAC inhibitors and various subtype-specific drugs.

Read the official press release highlighting this research.

Immune landscape of hepatoblastoma

doi: https://doi.org/10.1101/2023.06.28.546852

Krijgsman D#, Kraaier LJ#, Verdonschot M, Schubert SA, Duiker E, de Kleine R, de Meijer V, de Krijger RR, Zsiros J, Leusen J, Peng WC*, Vercoulen Y*. Hepatoblastoma exhibits a predominantly myeloid immune landscape and reveals opportunities for macrophage targeted immunotherapy. 2023. BioRxiv:

Immunotherapy is a type of cancer treatment that helps the immune system fight cancer. Our research shows that a common type of immunotherapy, which targets certain immune cells called T cells, will unlikely be effective for hepatoblastoma patients. However, hepatoblastomas have a high number of another type of immune cells called marcrophages. This finding opens up new possibilities for developing better treatments.

Long-term expansion of mouse hepatocyte organoids

doi: https://doi.org/10.1007/978-1-0716-2557-6_1

Kluiver TA, Kraaier LJ, Peng WC. Long-Term Expansion of Murine Primary Hepatocyte Organoids. Methods Mol Biol. 2022;2544:1-13.

In this book chapter, we describe a detailed protocol for the isolation and long-term culture of primary mouse hepatocytes. We are honored to be invited to publish our work in this edition on Hepatocytes (Methods in Molecular Biology), which described the most important methods in the field in the last 10 years.

Potential of hepatocyte organoid transplantation to treat liver disease

doi: https://doi.org/10.1038/s12276-021-00579-x

Peng WC, Kraaier LJ, Kluiver TA. Hepatocyte organoids and cell transplantation: What the future holds. Exp Mol Med. 2021;53(10):1512-1528.

In this review article, we focus on recent advances in establishing hepatocyte organoids and their potential applications in regenerative medicine. We discuss the suitability of cell replacement therapy to treat different types of liver diseases and the current state of cell transplantation of in vitro-expanded hepatocytes in mouse models. We are honored to be invited to contribute to this special issue on Methods in Organoids, which highlights the most significant and state-of-the-art methods in the organoid field.

Development of the first hepatocyte organoid model with high engraftment efficacy

doi: https://doi.org/10.1016/j.cell.2018.11.012

Peng WC*, Logan CY, Fish M, Anbarchian T, Aguisanda F, Alvarez A, Wu P, Jin Y, Zhu J, Li B, Grompe M, Wang B, Nusse R*. Inflammatory cytokine TNFa promotes the long-term expansion of primary hepatocytes in 3D culture. Cell. 2018. 175, 607–1619.e1615. (* corresponding authors)

We establish the first mouse hepatocyte organoid culture by employing tissue regenerative signals in the liver. More importantly, we demonstrate that these organoids are very efficient in engraftment in a mouse liver injury model. As a result, the donor cells support and maintain liver function when the host liver function is impaired. This paves the way for the use of lab grown organoids to study and treat various metabolic liver diseases.

Cancers

Our organoid models of hepatoblastoma are a reliable system for discovering new treatment options. Our models have been used to study innovative immune therapies. Additionally, genomics analysis of pediatric cancer patients has identified potentially pathogenic fusion, for example a novel TERT fusion linked to TERT overexpression in a patient with hepatic adenoma.

van Belzen IAEM, van Tuil M, Badloe S, Janse A, Verwiel ETP, Santoso M, de Vos S, Baker-Hernandez J, Kerstens HHD, Solleveld-Westerink N, Meister MT, Drost J, van den Heuvel-Eibrink MM, Merks JHM, Molenaar JJ, Peng WC, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors. Cell Genomics. 2024 Nov 13;4(11):100675.doi: https://doi.org/10.1016/j.xgen.2024.100675

Hernández-López P, van Diest E, Brazda P, Heijhuurs S, Meringa A, Hoorens van Heyningen L, Riillo C, Schwenzel C, Zintchenko M, Johanna I, Nicolasen MJT, Cleven A, Kluiver TA, Millen R, Zheng J, Karaiskaki F, Straetemans T, Clevers H, de Bree R, Stunnenberg HG, Peng WC, Roodhart J, Minguet S, Sebestyén Z, Beringer DX, Kuball J. Dual targeting of cancer metabolome and stress antigens affects transcriptomic heterogeneity and efficacy of engineered T cells. Nat Immunol. 2023 Nov 27. doi: https://doi.org/10.1038/s41590-023-01665-0

Cornel AM, van der Sman L, van Dinter JT, Arrabito M, Dünnebach E, Dautzenberg NMM, van Rijn JM, van den Beemt DAMH, Buhl JL, du Chatinier A, Barneh F, Lu Y, Lo Nigro L, Krippner-Heidenreich A, Hulleman E, Drost J, van Heesch SAAC, Heidenreich OT, Peng WC, Nierkens S, Targeting pediatric cancers via T-cell recognition of the monomorphic MHC class I related protein MR1. Journal of ImmunoTherapy for Cancer, 2024 Mar 21;12(3):e007538. doi: https://doi.org/10.1136/jitc-2023-007538

van Belzen IAEM, Cai C, van Tuil M,Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HHD, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. BMC Cancer. 2023;23(1):618. Published 2023 Jul 3. doi: https://doi.org/10.1186/s12885-023-11054-3

Regenerative medicine

Our mouse hepatocyte organoid models are a reliable system for discovering new biology and treatment options. They have been used to study novel extracellular vesicle for protein/RNA delivery, next-gen WNT surrogate and for investigating cell division and hepatocyte ploidy.

Ilahibaks NF, Kluiver TA, de Jong OG, de Jager S, Schiffelers RM, Vader P, Peng WC, Lei Z, Sluijter JPG. Extracellular vesicle-mediated delivery of CRISPR/Cas9 ribonucleoprotein complex targeting Pcsk9 in mouse hepatocytes. Journal of Extracellular Vesicles, 024 Jan;13(1):e12389.

doi: https://doi.org/10.1002/jev2.12389

Jin Y, Anbarchian T, Wu P, Sarkar A, Fish M, Peng WC, & Nusse R. Wnt signaling regulates hepatocyte cell division by a transcriptional repressor cascade. Proceedings of the National Academy of Sciences of the United States of America, 2022, 119(30). doi: https://doi.org/10.1073/pnas.2203849119

Marsee A, Roos FJM, Verstegen MMA, HPB Organoid Consortium, Gehart H, de Koning E, Lemaigre F, Forbes SJ, Peng WC, Huch M, Takebe T, Vallier L, Clevers H, van der Laan LJW, Spee B. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell. 2021 May 6;28(5):816-832. doi: https://doi.org/10.1016/j.stem.2021.04.005

Miao Y, Ha A, de Lau W, Yuki K, Santos AJM, You C, Geurts MH, Puschhof J, Pleguezuelos-Manzano C, Peng WC, Senlice R, Piani C, Buikema JW, Gbenedio OM, Vallon M, Yuan J, de Haan S, Hemrika W, Rösch K, Dang LT, Baker D, Ott M, Depeille P, Wu SM, Drost J, Nusse R, Roose JP, Piehler J, Boj SF, Janda CY, Clevers H, Kuo CJ, Garcia KC. Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo. Cell Stem Cell. 2020 Nov 5;27(5):840-851.e6. doi: https://doi.org/10.1016/j.stem.2020.07.020

Mouse cell atlas

We performed single cell transcriptomic profiling of liver tissues for the mouse cell atlas project, which aim to study aging/parabiosis processes. Tabula Muris Consortium is a collaborative project between Stanford University, UCSF and the Chan Zuckerberg Initiative (CZI) Biohub.

Tabula Muris Consortium. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature. 2020 Jul;583(7817):590-595. doi: https://doi.org/10.1038/s41586-020-2496-1

Schaum N, Lehallier B, Hahn O, Pálovics R, Hosseinzadeh S, Lee SE, Sit R, Lee DP, Losada PM, Zardeneta ME, Fehlmann T, Webber JT, McGeever A, Calcuttawala K, Zhang H, Berdnik D, Mathur V, Tan W, Zee A, Tan M, Tabula Muris Consortium, Pisco AO, Karkanias J, Neff NF, Keller A, Darmanis S, Quake SR, Wyss-Coray T. Ageing hallmarks exhibit organ-specific temporal signatures. Nature.

2020 Jul;583(7817):596-602. doi: https://doi.org/10.1038/s41586-020-2499-y

Tabula Muris Consortium. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature. 2018 Oct;562(7727):367-372. doi: https://doi.org/10.1038/s41586-018-0590-4

Structural biology of WNT and FGFR signaling

We used x-ray crystallography to unravel the molecular mechanism of Wnt signaling regulation by LGR5, R-spondin and ZNRF3, which are crucial for adult stem cell proliferation. These projects were performed in collaboration with the Clevers lab. Additionally, we used infrared spectroscopy to examine FGFR3 transmembrane peptide mutations linked to dwarfism, initiated in the Torres lab.

de Lau W, Peng WC, Gros P, Clevers H. The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength. Genes & development. 2014 Feb 15;28(4):305-16. doi: https://doi.org/10.1101/gad.235473.113

Peng WC#, de Lau W#, Forneris F, Granneman JCM, Huch M, Clevers H, Gros P. Structure of Stem Cell Growth Factor R-spondin 1 in Complex with the Ectodomain of Its Receptor LGR5. Cell Reports. 2013 Jun 27;3(6):1885-92. doi: https://doi.org/10.1016/j.celrep.2013.06.009

Peng WC, de Lau W, Madoori PK, Forneris F, Granneman JCM, Clevers H, Gros P. Structures of Wnt-antagonist ZNRF3 and its complex with R-spondin 1 and implications for signaling. PLoS ONE. 2013 Dec 12;8(12):e83110. doi: https://doi.org/10.1371/journal.pone.0083110

Peng WC, Lin X, Torres J. The strong dimerization of the transmembrane domain of the fibroblast growth factor receptor 3 (FGFR3) is modulated by C-terminal juxtamembrane residues. Protein Science. 2009 Feb;18(2):450-9. doi: https://doi.org/10.1002/pro.65

Priya R, Tadwal, VS, Roessle MW, Gayen S, Hunke C, Peng WC, Torres J, Grüber G. Low resolution structure of subunit b (b (22-156)) of Escherichia coli F(1)F(O) ATP synthase in solution and the b-delta assembly. Journal of Bioenergetics and Biomembranes. 2008 Aug;40(4):245-55. doi: https://doi.org/10.1007/s10863-008-9154-x