Transfection into Organoids by Electroporation

Recapitulating the adenoma–carcinoma sequence by selection of four spontaneous oncogenic mutations in mismatch-repair-deficient human colon organoids

Mizutani T, Boretto M, Lim S, Drost J, González DM, Oka R, Geurts MH, Begthel H, Korving J, van Es JH, van Boxtel R, Clevers H.

Nat Cancer. 2024 Nov 1.

Human Gastric Multi-Regional Assembloids Favour Functional Parietal Maturation and Allow Modelling of Antral Foveolar Hyperplasia

Brendan C Jones, Giada Benedetti, Giuseppe Calà, Lucinda Tullie, Ian C Simcoc, Roberto Lutman, Monika Balys, Ramin Amiri, Jahangir Sufi, Owen Arthurs, Simon Eaton, Glenn Anderson, Nicola Elvassore, Vivian SW Li, Kelsey DJ Jones, Christopher J. Tape, Camilla Luni, Giovanni Giuseppe Giobbe, Paolo De Coppi

bioRxiv, July 11, 2024

Clonal Origin and Lineage Ambiguity in Mixed Neuroendocrine Carcinoma of the Uterine Cervix

Masamune Masuda, Keita Iida, Sadahiro Iwabuchi, Mie Tanaka, Satoshi Kubota, Hiroyuki Uematsu, Kunishige Onuma, Yoji Kukita, Kikuya Kato, Shoji Kamiura, Aya Nakajima, Roberto Coppo, Mizuki Kanda, Kiyoshi Yoshino, Yutaka Ueda, Eiichi Morii, Tadashi Kimura, Jumpei Kondo, Mariko Okada-Hatakeyama, Shinichi Hashimoto, Masahiro Inoue

Am J Pathol . 2024 Mar;194(3):415-429.

Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells

Hermosilla VE, Gyenis L, Rabalski AJ, Armijo ME, Sepúlveda P, Duprat F, Benítez-Riquelme D, Fuentes-Villalobos F, Quiroz A, Hepp MI, Farkas C, Mastel M, González-Chavarría I, Jackstadt R, Litchfield DW, Castro AF, Pincheira R.

Cell Death Dis. 2024 Mar 16;15(3):223.

An alternative splicing signature defines the basallike phenotype and predicts worse clinical outcome in pancreatic cancer

Ruta V, Naro C, Pieraccioli M, Leccese A, Archibugi L, Cesari E, Panzeri V, Allgöwer C, Arcidiacono PG, Falconi M, Carbone C, Tortora G, Borrelli F, Attili F, Spada C, Quero G, Alfieri S, Doglioni C, Kleger A, Capurso G, Sette C.

Cell Rep Med. 2024 Feb 20;5(2):101411.

Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma

Ziman B, Yang Q, Zheng Y, Sheth M, Nam C, Zhao H, Zhang L, Hu B, Bhowmick NA, Sinha UK, Lin DC.

Cell Death Dis. 2024 Feb 19;15(2):152.

Human conjunctiva organoids to study ocular surface homeostasis and disease

Bannier-Hélaouët M, Korving J, Ma Z, Begthel H, Giladi A, Lamers MM, van de Wetering WJ, Yawata N, Yawata M, LaPointe VLS, Dickman MM, Kalmann R, Imhoff SM, van Es JH, López-Iglesias C, Peters PJ, Haagmans BL, Wu W, Clevers H.

Cell Stem Cell. 2024 Feb 1;31(2):227-243.e12.

Human fetal brain self-organizes into long-term expanding organoids

Hendriks D, Pagliaro A, Andreatta F, Ma Z, van Giessen J, Massalini S, López-Iglesias C, van Son GJF, DeMartino J, Damen JMA, Zoutendijk I, Staliarova N, Bredenoord AL, Holstege FCP, Peters PJ, Margaritis T, Chuva de Sousa Lopes S, Wu W, Clevers H, Artegiani B.

Cell. 2024 Jan 4:S0092-8674(23)01344-2.

Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2

Colozza G, Lee H, Merenda A, Wu SS, Català-Bordes A, Radaszkiewicz TW, Jordens I, Lee JH, Bamford AD, Farnhammer F, Low TY, Maurice MM, Bryja V, Kim J, Koo BK.

Sci Adv. 2023 Nov 24;9(47):eadh9673.

Engineered human hepatocyte organoids enable CRISPR-based target discovery and drug screening for steatosis

Hendriks D, Brouwers JF, Hamer K, Geurts MH, Luciana L, Massalini S, López-Iglesias C, Peters PJ, Rodríguez-Colman MJ, Chuva de Sousa Lopes S, Artegiani B, Clevers H.

Nat Biotechnol. 2023 Nov;41(11):1567-1581.

Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model

Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ.

Sci Transl Med . 2022 Nov 30;14(673):eabq6146.

Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2

Colozza G, Lee H, Merenda A, Wu SS, Català-Bordes A, Radaszkiewicz TW, Jordens I, Lee JH, Bamford AD, Farnhammer F, Low TY, Maurice MM, Bryja V, Kim J, Koo BK

Sci Adv. 2023 Nov 24;9(47):eadh9673.

Engineered human hepatocyte organoids enable CRISPR-based target discovery and drug screening for steatosis

endriks D, Brouwers JF, Hamer K, Geurts MH, Luciana L, Massalini S, López-Iglesias C, Peters PJ, Rodríguez-Colman MJ, Chuva de Sousa Lopes S, Artegiani B, Clevers H.

Nat Biotechnol. 2023 Nov;41(11):1567-1581.

One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids

Geurts MH, Gandhi S, Boretto MG, Akkerman N, Derks LLM, van Son G, Celotti M, Harshuk-Shabso S, Peci F, Begthel H, Hendriks D, Schürmann P, Andersson-Rolf A, Chuva de Sousa Lopes SM, van Es JH, van Boxtel R, Clevers H.

Nat Commun. 2023 Aug 17;14(1):4998.

Patient-derived head and neck cancer organoids allow treatment stratification and serve as a tool for biomarker validation and identification

Millen R, De Kort WWB, Koomen M, van Son GJF, Gobits R, Penning de Vries B, Begthel H, Zandvliet M, Doornaert P, Raaijmakers CPJ, Geurts MH, Elias SG, van Es RJJ, de Bree R, Devriese LA, Willems SM, Kranenburg O, Driehuis E, Clevers H.

Med. 2023 May 12;4(5):290-310.e12.

Establishment, Maintenance, Differentiation, Genetic Manipulation, and Transplantation of Mouse and Human Lacrimal Gland Organoids

Bannier-Hélaouët M, Geurts MH, Korving J, Begthel H, Clevers H.

J Vis Exp. 2023 Feb 3:(192).

SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis

Loevenich LP, Tschurtschenthaler M, Rokavec M, Silva MG, Jesinghaus M, Kirchner T, Klauschen F, Saur D, Neumann J, Hermeking H, Jung P.

Cancer Res. 2022 Dec 16;82(24):4604-4623.

Multiparametric and accurate functional analysis of genetic sequence variants using CRISPR-Select

Niu Y, Ferreira Azevedo CA, Li X, Kamali E, Haagen Nielsen O, Storgaard Sørensen C, Frödin M.

Nat Genet. 2022 Dec;54(12):1983-1993.

Mapping prohormone processing by proteases in human enteroendocrine cells using genetically engineered organoid models

Beumer J, Bauzá-Martinez J, Veth TS, Geurts V, Boot C, Gilliam-Vigh H, Poulsen SS, Knop FK, Wu W, Clevers H.

Proc Natl Acad Sci U S A. 2022 Nov 16;119(46):e2212057119.

Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis

Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, Narres D, Neyazi M, Kayisoglu Ö, Sell T, Blüthgen N, Morkel M, Wiegering A, Germer CT, Kircher S, Rosenwald A, Saliba AE, Bartfeld S.

Nat Commun. 2022 Oct 5;13(1):5878.

Differentiation and CRISPR-Cas9-mediated genetic engineering of human intestinal organoids

Martinez-Silgado A, Yousef Yengej FA, Puschhof J, Geurts V, Boot C, Geurts MH, Rookmaaker MB, Verhaar MC, Beumer J, Clevers H.

STAR Protoc. 2022 Aug 18;3(3):101639.

GREM1 is required to maintain cellular heterogeneity in pancreatic cancer

Lan L, Evan T, Li H, Hussain A, Ruiz EJ, Zaw Thin M, Ferreira RMM, Ps H, Riising EM, Zen Y, Almagro J, Ng KW, Soro-Barrio P, Nelson J, Koifman G, Carvalho J, Nye EL, He Y, Zhang C, Sadanandam A, Behrens A.

Nature. 2022 Jul;607(7917):163-168.

USP25 promotes pathological HIF-1-driven metabolic reprogramming and is a potential therapeutic target in pancreatic cancer

Nelson JK, Thin MZ, Evan T, Howell S, Wu M, Almeida B, Legrave N, Koenis DS, Koifman G, Sugimoto Y, Llorian Sopena M, MacRae J, Nye E, Howell M, Snijders AP, Prachalias A, Zen Y, Sarker D, Behrens A.

Nat Commun. 2022 Apr 19;13(1):2070.

BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states

Beumer J, Puschhof J, Yengej FY, Zhao L, Martinez-Silgado A, Blotenburg M, Begthel H, Boot C, van Oudenaarden A, Chen YG, Clevers H.

Cell Rep. 2022 Mar 1;38(9):110438.

Mutation-specific reporter for optimization and enrichment of prime editing

Schene IF, Joore IP, Baijens JHL, Stevelink R, Kok G, Shehata S, Ilcken EF, Nieuwenhuis ECM, Bolhuis DP, van Rees RCM, Spelier SA, van der Doef HPJ, Beekman JM, Houwen RHJ, Nieuwenhuis EES, Fuchs SA.

Nat Commun. 2022 Mar 1;13(1):1028.

Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage

Bollen Y, Hageman JH, van Leenen P, Derks LLM, Ponsioen B, Buissant des Amorie JR, Verlaan-Klink I, van den Bos M, Terstappen LWMM, van Boxtel R, Snippert HJG.

PLoS Biol. 2022 Jan 28;20(1):e3001527.

Disease Modeling on Tumor Organoids Implicates AURKA as a Therapeutic Target in Liver Metastatic Colorectal Cancer

Boos SL, Loevenich LP, Vosberg S, Engleitner T, Öllinger R, Kumbrink J, Rokavec M, Michl M, Greif PA, Jung A, Hermeking H, Neumann J, Kirchner T, Rad R, Jung P.

Cell Mol Gastroenterol Hepatol. 2022;13(2):517-540.

Modelling of primary ciliary dyskinesia using patient-derived airway organoids

van der Vaart J, Böttinger L, Geurts MH, van de Wetering WJ, Knoops K, Sachs N, Begthel H, Korving J, Lopez-Iglesias C, Peters PJ, Eitan K, Gileles-Hillel A, Clevers H.

EMBO Rep. 2021 Dec 6;22(12):e52058.

Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer

Westcott PMK, Sacks NJ, Schenkel JM, Ely ZA, Smith O, Hauck H, Jaeger AM, Zhang D, Backlund CM, Beytagh MC, Patten JJ, Elbashir R, Eng G, Irvine DJ, Yilmaz OH, Jacks T.

Nat Cancer. 2021 Oct;2(10):1071-1085.

A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses

Joep Beumer, Maarten H Geurts, Mart M Lamers, Jens Puschhof, Jingshu Zhang, Jelte van der Vaart, Anna Z Mykytyn, Tim I Breugem, Samra Riesebosch, Debby Schipper, Petra B van den Doel, Wim de Lau, Cayetano Pleguezuelos-Manzano, Georg Busslinger, Bart L Haagmans, Hans Clevers

Nat Commun. 2021 Sep 17;12(1):5498.

A protocol for efficient CRISPR-Cas9-mediated knock-in in colorectal cancer patient-derived organoids

Okamoto T, Natsume Y, Yamanaka H, Fukuda M, Yao R.

STAR Protoc. 2021 Sep 16;2(4):100780.

Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Bollen Y, Stelloo E, van Leenen P, van den Bos M, Ponsioen B, Lu B, van Roosmalen MJ, Bolhaqueiro ACF, Kimberley C, Mossner M, Cross WCH, Besselink NJM, van der Roest B, Boymans S, Oost KC, de Vries SG, Rehmann H, Cuppen E, Lens SMA, Kops GJPL, Kloosterman WP, Terstappen LWMM, Barnes CP, Sottoriva A, Graham TA, Snippert HJG.

Nat Genet. 2021 Aug;53(8):1187-1195.

Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids

Nat Protoc. 2021 Apr;16(4):1936-1965.

Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids

Geurts MH, de Poel E, Pleguezuelos-Manzano C, Oka R, Carrillo L, Andersson-Rolf A, Boretto M, Brunsveld JE, van Boxtel R, Beekman JM, Clevers H.

Life Sci Alliance. 2021 Aug 9;4(10):e202000940.

Exploring the human lacrimal gland using organoids and single-cell sequencing

Bannier-Hélaouët M, Post Y, Korving J, Trani Bustos M, Gehart H, Begthel H, Bar-Ephraim YE, van der Vaart J, Kalmann R, Imhoff SM, Clevers H.

Cell Stem Cell. 2021 Jul 1;28(7):1221-1232.e7

Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids

Dekkers JF, van Vliet EJ, Sachs N, Rosenbluth JM, Kopper O, Rebel HG, Wehrens EJ, Piani C, Visvader JE, Verissimo CS, Boj SF, Brugge JS, Clevers H, Rios AC.

Nat Protoc. 2021 Apr;16(4):1936-1965.

Mutational inactivation of Apc in the intestinal epithelia compromises cellular organisation

Rannikmae H, Peel S, Barry S, Senda T, de la Roche M.

J Cell Sci. 2021 Jan 27;134(2):jcs250019.

Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver

Hendriks D, Artegiani B, Hu H, Chuva de Sousa Lopes S, Clevers H.

Nat Protoc . 2021 Jan;16(1):182-217

Introducing the Stem Cell ASCL2 Reporter STAR into Intestinal Organoids

Heinz MC, Oost KC, Snippert HJG.

STAR Protoc. 2020 Oct 8;1(3):100126.

Dedifferentiation of neuroendocrine carcinoma of the uterine cervix in hypoxia

Satoshi Kubota, Mie Tanaka, Hiroko Endo, Yu Ito, Kunishige Onuma, Yutaka Ueda, Shoji Kamiura, Kiyoshi Yoshino, Tadashi Kimura, Jumpei Kondo, Masahiro Inoue

Biochem Biophys Res Commun. 2020 Apr 2;524(2):398-404.

Organoid Derivation and Orthotopic Xenotransplantation for Studying Human Intestinal Stem Cell Dynamics

Shinya Sugimoto, Masayuki Fujii, Toshiro Sato

Methods Mol Biol. 2020;2171:303-320.

Fast and Efficient Generation of Knock-In Human Organoids Using Homology-Independent CRISPR-Cas9 Precision Genome Editing

Benedetta Artegiani, Delilah Hendriks, Joep Beumer, Rutger Kok, Xuan Zheng, Indi Joore, Susana Chuva de Sousa Lopes, Jeroen van Zon, Sander Tans, Hans Clevers

Nat Cell Biol 2020 Mar 2[Online ahead of print]

Universal and Efficient Electroporation Protocol for Genetic Engineering of Gastrointestinal Organoids

Anne-Marlen Gaebler, Alexander Hennig, Katharina Buczolich, Jürgen Weitz, Thilo Welsch, Daniel E Stange, Kristin Pape

J Vis Exp. 2020 Feb 18;(156).

Chromosome Engineering of Human Colon-Derived Organoids to Develop a Model of Traditional Serrated Adenoma

Kenta Kawasaki, Masayuki Fujii, Shinya Sugimoto, Keiko Ishikawa, Mami Matano, Yuki Ohta, Kohta Toshimitsu, Sirirat Takahashi, Naoki Hosoe, Shigeki Sekine, Takanori Kanai, Toshiro Sato

Gastroenterology, 158 (3), 638-651.e8 Feb 2020

RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer

Spit M, Fenderico N, Jordens I, Radaszkiewicz T, Lindeboom RG, Bugter JM, Cristobal A, Ootes L, van Osch M, Janssen E, Boonekamp KE, Hanakova K, Potesil D, Zdrahal Z, Boj SF, Medema JP, Bryja V, Koo BK, Vermeulen M, Maurice MM.

EMBO J. 2020 Sep 15;39(18):e103932.

Human liver ductal organoids: Single intact ordanoids electroporation by CUY650P1 electrodes
Human hepatocyte organoids: Dissociated single cells cuvette electroporation

Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

Benedetta Artegiani, Lisa van Voorthuijsen, Rik G H Lindeboom, Daniëlle Seinstra, Inha Heo, Pablo Tapia, Carmen López-Iglesias, Daniel Postrach, Talya Dayton, Rurika Oka, Huili Hu, Ruben van Boxtel, Johan H van Es, Johan Offerhaus, Peter J Peters, Jacco van Rheenen, Michiel Vermeulen, Hans Clevers

Cell Stem Cell, 24 (6), 927-943.e6 2019 Jun 6

An Organoid Platform for Ovarian Cancer Captures Intra- And Interpatient Heterogeneity

Oded Kopper, Chris J de Witte, Kadi Lõhmussaar, Jose Espejo Valle-Inclan, Nizar Hami, Lennart Kester, Anjali Vanita Balgobind, Jeroen Korving, Natalie Proost, Harry Begthel, Lise M van Wijk, Sonia Aristín Revilla, Rebecca Theeuwsen, Marieke van de Ven, Markus J van Roosmalen, Bas Ponsioen, Victor W H Ho, Benjamin G Neel, Tjalling Bosse, Katja N Gaarenstroom, Harry Vrieling, Maaike P G Vreeswijk, Paul J van Diest, Petronella O Witteveen, Trudy Jonges, Johannes L Bos, Alexander van Oudenaarden, Ronald P Zweemer, Hugo J G Snippert, Wigard P Kloosterman, Hans Clevers

Nat Med, 25 (5), 838-849 May 2019

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition.

Fujii M, Matano M, Toshimitsu K, Takano A, Mikami Y, Nishikori S, Sugimoto S, Sato T

Cell Stem Cell. 2018 Dec 6;23(6):787-793.e6.

Intestinal Failure and Aberrant Lipid Metabolism in Patients With DGAT1 Deficiency

van Rijn JM, Ardy RC, Kuloğlu Z, Härter B, van Haaften-Visser DY, van der Doef HPJ, van Hoesel M, Kansu A, van Vugt AHM, Thian M, Kokke FTM, Krolo A, Başaran MK, Kaya NG, Aksu AÜ, Dalgıç B, Ozcay F, Baris Z, Kain R, Stigter ECA, Lichtenbelt KD, Massink MPG, Duran KJ, Verheij JBGM, Lugtenberg D, Nikkels PGJ, Brouwer HGF, Verkade HJ, Scheenstra R, Spee B, Nieuwenhuis EES, Coffer PJ, Janecke AR, van Haaften G, Houwen RHJ, Müller T, Middendorp S, Boztug K

Gastroenterology. 2018 Jul;155(1):130-143.e15.

Activation of WNT/β-catenin signaling results in resistance to a dual PI3K/mTOR inhibitor in colorectal cancer cells harboring PIK3CA mutations.

Park YL, Kim HP, Cho YW, Min DW, Cheon SK, Lim YJ, Song SH, Jin Kim S, Han SW, Park KJ, Kim TY

Int J Cancer. 2019 Jan 15;144(2):389-401.

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity.

Sachs N, de Ligt J, Kopper O, Gogola E, Bounova G, Weeber F, Balgobind AV, Wind K, Gracanin A, Begthel H, Korving J, van Boxtel R, Duarte AA, Lelieveld D, van Hoeck A, Ernst RF, Blokzijl F, Nijman IJ, Hoogstraat M, van de Ven M, Egan DA, Zinzalla V, Moll J, Boj SF, Voest EE, Wessels L, van Diest PJ, Rottenberg S, Vries RGJ, Cuppen E, Clevers H.

Cell. 2018 Jan 11;172(1-2):373-386.e10.

A Protocol for Multiple Gene Knockout in Mouse Small Intestinal Organoids Using a CRISPR-concatemer

Merenda A, Andersson-Rolf A, Mustata RC, Li T, Kim H, Koo BK

J Vis Exp. 2017 Jul 12;(125).

Efficient genetic engineering of human intestinal organoids using electroporation

Fujii M, Matano M, Nanki K, Sato T

Nat Protoc. 2015 Oct;10(10):1474-85. Epub 2015 Sep 3.

Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids.

Matano M, Date S, Shimokawa M, Takano A, Fujii M, Ohta Y, Watanabe T, Kanai T, Sato T.

Nat Med. 2015 Mar;21(3):256-62.