NEPA21 Organoid Bibliography

Here is a full bibliography-style listing based on NEPA21 organoid pubblications, organised into readable sections.

This page is intended as a bibliography companion to the main organoid workflow page. It groups the NEPA21 publications across intestinal, colorectal, neuronal, airway, gastric, pancreatic, hepatic, breast, ovarian, fallopian tube, murine, and related organoid systems.

Use it as a reference page for readers who want the publication footprint behind NEPA21 organoid workflows in a dedicated, browseable format.

Full bibliography page

Grouped by organoid context

Publication List as a browseable resource

Jump to Bibliography Sections

Request: Help or Free NEPA21 Trial

About this bibliography page

This version is designed as a dedicated bibliography page rather than a workflow overview. The publication entries are grouped for readability.

Some entries sit across more than one biological context. Where that happened, they have been placed in the section where they are likely to be most useful to readers.

1. Human intestinal & colorectal organoid bibliography

Human small intestinal, intestinal, gut, colon, colorectal, large-intestinal, duodenal, and related GI organoid publications referenced in the PDF.

Human small intestinal / intestinal

A tunable human intestinal organoid system achieves controlled balance between self-renewal and differentiation. Yang L, Wang X, Zhou X, Chen H, Song S, Deng L, Yao Y, Yin X. Nat Commun. 2025 Jan 2;16(1):315.
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.
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.
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.
Organoid Derivation and Orthotopic Xenotransplantation for Studying Human Intestinal Stem Cell Dynamics. Sugimoto S, Fujii M, Sato T. Methods Mol Biol. 2020;2171:303-320.
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.
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.
A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses. Beumer J, Geurts MH, Lamers MM, Puschhof J, Zhang J, van der Vaart J, Mykytyn AZ, Breugem TI, Riesebosch S, Schipper D, van den Doel PB, de Lau W, Pleguezuelos-Manzano C, Busslinger G, Haagmans BL, Clevers H. Nat Commun. 2021 Sep 17;12(1):5498.
A xenogeneic-free system generating functional human gut organoids from pluripotent stem cells. Uchida H, Machida M, Miura T, Kawasaki T, Okazaki T, Sasaki K, Sakamoto S, Ohuchi N, Kasahara M, Umezawa A, Akutsu H. JCI Insight. 2017 Jan 12;2(1):e86492.
Fast and Efficient Generation of Knock-In Human Organoids Using Homology-Independent CRISPR-Cas9 Precision Genome Editing. Artegiani B, Hendriks D, Beumer J, Kok R, Zheng X, Joore I, Chuva de Sousa Lopes S, van Zon J, Tans S, Clevers H. Nat Cell Biol. 2020 Mar 2 [Online ahead of print].
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.
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.
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.

Human colon / colorectal / large-intestinal / CRC

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.
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.
Chromosome Engineering of Human Colon-Derived Organoids to Develop a Model of Traditional Serrated Adenoma. Kawasaki K, Fujii M, Sugimoto S, Ishikawa K, Matano M, Ohta Y, Toshimitsu K, Takahashi S, Hosoe N, Sekine S, Kanai T, Sato T. Gastroenterology. 2020 Feb;158(3):638-651.e8.
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.
Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance. Esposito A, Agostini A, Quero G, Piro G, Priori L, Caggiano A, Scaglione G, Battaglia A, Calegari MA, Salvatore L, Bensi M, Maratta MG, Ceccarelli A, Trovato G, Genovese G, Gurreri E, Ascrizzi S, Martini M, Fiorillo C, Fattorossi A, De Sanctis F, Ugel S, Corbo V, Alfieri S, Tortora G, Carbone C. Cell Death Dis. 2024 Dec 4;15(12):878.
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Kayhanian H, Cross W, van der Horst SEM, Barmpoutis P, Lakatos E, Caravagna G, Zapata L, Van Hoeck A, Middelkamp S, Litchfield K, Steele C, Waddingham W, Patel D, Milite S, Jin C, Baker AM, Alexander DC, Khan K, Hochhauser D, Novelli M, Werner B, van Boxtel R, Hageman JH, Buissant des Amorie JR, Linares J, Ligtenberg MJL, Nagtegaal ID, Laclé MM, Moons LMG, Brosens LAA, Pillay N, Sottoriva A, Graham TA, Rodriguez-Justo M, Shiu KK, Snippert HJG, Jansen M. Nat Genet. 2024 Jul;56(7):1420-1433.
A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LL, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, Weingarth M, Vermeulen M, Klumperman J, Maurice MM. Life Sci Alliance. 2023 Aug 17;6(11):e202302058.
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.
Disease Modelling 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.
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.
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, Kim SJ, Han SW, Park KJ, Kim TY. Int J Cancer. 2019 Jan 15;144(2):389-401.
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.

GI protocol / electroporation-linked bibliography

Universal and Efficient Electroporation Protocol for Genetic Engineering of Gastrointestinal Organoids. Gaebler AM, Hennig A, Buczolich K, Weitz J, Welsch T, Stange DE, Pape K. J Vis Exp. 2020 Feb 18;(156).

2. Brain, neuronal, airway, ocular, head & neck bibliography

Neuronal, forebrain, fetal brain, airway, conjunctival, and head-and-neck linked organoid publications in the source bibliography.

Brain / neuronal / forebrain

Calcium-Enhanced Medium-Based Delivery of Splice Modulating Antisense Oligonucleotides in 2D and 3D hiPSC-Derived Neuronal Models. Buijsen RAM, van der Graaf LM, Kuijper EC, Pepers BA, Daoutsali E, Weel L, Raz V, Parfitt DA, van Roon-Mom WMC. Biomedicines. 2024 Aug 23;12(9):1933.
Efficient Derivation of Sympathetic Neurons From Human Pluripotent Stem Cells With a Defined Condition. Kirino K, Nakahata T, Taguchi T, Saito MK. Sci Rep. 2018 Aug 27;8(1):12865.
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.
Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders. Yoon JG, Jang H, Lee S, Jang SS, Park S, Cho J, Kim M, Han J, Yun H, Kim MJ, Kim SY, Kim WJ, Cho A, Lee JS, Choi M, Fernandez-Jaen A, Silva S, Uribe-San-Martín R, Cantillano C, Miyake N, Lim BC, Ko JM, Kim KJ, Yoon KJ, Chae JH. Genome Med. 2025 Aug 6;17(1):86.

Airway / respiratory

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.
Drug Repurposing for Cystic Fibrosis: Identification of Drugs That Induce CFTR-Independent Fluid Secretion in Nasal Organoids. Rodenburg LWW, Delpiano L, Railean V, Centeio R, Pinto MC, Smits SMA, van der Windt IS, van Hugten CFJ, van Beuningen SFB, Rodenburg RNP, van der Ent CK, Amaral MD, Kunzelmann K, Gray MA, Beekman JM, Amatngalim GD. Int J Mol Sci. 2022 Oct 21;23(20):12657.

Ocular / conjunctiva

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.

Head, neck, cervix, neuroendocrine / spheroid-linked

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.
Clonal Origin and Lineage Ambiguity in Mixed Neuroendocrine Carcinoma of the Uterine Cervix. Masuda M, Iida K, Iwabuchi S, Tanaka M, Kubota S, Uematsu H, Onuma K, Kukita Y, Kato K, Kamiura S, Nakajima A, Coppo R, Kanda M, Yoshino K, Ueda Y, Morii E, Kimura T, Kondo J, Okada-Hatakeyama M, Hashimoto S, Inoue M. Am J Pathol. 2024 Mar;194(3):415-429.
Dedifferentiation of neuroendocrine carcinoma of the uterine cervix in hypoxia. Kubota S, Tanaka M, Endo H, Ito Y, Onuma K, Ueda Y, Kamiura S, Yoshino K, Kimura T, Kondo J, Inoue M. Biochem Biophys Res Commun. 2020 Apr 2;524(2):398-404.

3. Gastric, pancreatic, hepatic, esophageal & related bibliography

Gastric, pancreatic, hepatocyte, fetal hepatocyte, liver, esophageal adenocarcinoma, and related organoid publications from the PDF.

Pancreatic / pancreatic cancer

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.
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.
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.
SPP1 is required for maintaining mesenchymal cell fate in pancreatic cancer. Li H, Lan L, Chen H, Zaw Thin M, Ps H, Nelson JK, Evans IM, Ruiz EJ, Cheng R, Tran L, Allen M, Ma J, Yi T, Wang C, He Y, Guppy N, Sadanandam A, Lin SZ, Zhang C, Behrens A. Nature. 2025 Dec;648(8092):203-209.

Gastric / GI / esophageal / cholangiocarcinoma-linked

Universal and Efficient Electroporation Protocol for Genetic Engineering of Gastrointestinal Organoids. Gaebler AM, Hennig A, Buczolich K, Weitz J, Welsch T, Stange DE, Pape K. J Vis Exp. 2020 Feb 18;(156).
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.
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.
Human Gastric Multi-Regional Assembloids Favour Functional Parietal Maturation and Allow Modelling of Antral Foveolar Hyperplasia. Jones BC, Benedetti G, Calà G, Tullie L, Simcoc IC, Lutman R, Balys M, Amiri R, Sufi J, Arthurs O, Eaton S, Anderson G, Elvassore N, Li VSW, Jones KDJ, Tape CJ, Luni C, Giobbe GG, De Coppi P. bioRxiv. July 11, 2024.
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.

Hepatic / hepatocyte / liver

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.
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. 2020 Nov 27.
Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids. Artegiani B, van Voorthuijsen L, Lindeboom RGH, Seinstra D, Heo I, Tapia P, López-Iglesias C, Postrach D, Dayton T, Oka R, Hu H, van Boxtel R, van Es JH, Offerhaus JH, Peters PJ, van Rheenen J, Vermeulen M, Clevers H. Cell Stem Cell. 2019 Jun 6;24(6):927-943.e6.
Human liver ductal organoids: Single intact ordanoids electroporation by CUY650P1 electrodes.
Human hepatocyte organoids: Dissociated single cells cuvette electroporation.

4. Breast, ovarian, fallopian tube, endometrial & related bibliography

Breast cancer organoids, ovarian and fallopian-tube models, endometrial organoids, and related publications.

Breast

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.
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.

Fallopian tube / ovarian / serous ovarian cancer

mTOR-mediated p62/SQSTM1 stabilization confers a robust survival mechanism for ovarian cancer. Tamura T, Nagai S, Masuda K, Imaeda K, Sugihara E, Yamasaki J, Kawaida M, Otsuki Y, Suina K, Nobusue H, Akahane T, Chiyoda T, Kisu I, Kobayashi Y, Banno K, Sakurada K, Okita H, Yamaguchi R, Ahmed AA, Yamagami W, Saya H, Aoki D, Nagano O. Cancer Lett. 2025 Feb 17:217565.
LCN2-mediated ferroptosis resistance in tissue homeostasis and early-stage tumorigenesis of the fallopian tube epithelium. Imaeda K, Tamura T, Nagai S, Sugihara E, Yamasaki J, Otsuki Y, Nakamura K, Takeda T, Nakamura K, Nogami Y, Tsuji K, Chiyoda T, Kisu I, Kobayashi Y, Banno K, Yamaguchi R, Sakurada K, Saya H, Aoki D, Ahmed AA, Nagano O, Masuda K, Yamagami W. iScience. 2025 May 13;28(6):112654.
An Organoid Platform for Ovarian Cancer Captures Intra- And Interpatient Heterogeneity. Kopper O, de Witte CJ, Lõhmussaar K, Espejo Valle-Inclan J, Hami N, Kester L, Balgobind AV, Korving J, Proost N, Begthel H, van Wijk LM, Aristín Revilla S, Theeuwsen R, van de Ven M, van Roosmalen MJ, Ponsioen B, Ho VWH, Neel BG, Bosse T, Gaarenstroom KNG, Vrieling H, Vreeswijk MPG, van Diest PJ, Witteveen POW, Jonges T, Bos JL, van Oudenaarden A, Zweemer RP, Snippert HJG, Kloosterman WP, Clevers H. Nat Med. 2019 May;25(5):838-849.
Organoid platinum-resistance model identifies KRT17 as a biomarker of targeted therapy in ovarian cancer. Reichenbach J, Schmid J, Hierlmayer S, Zhang T, Piga I, Geweniger S, Fischer J, Davesar A, Vasovic N, Chelariu-Raicu A, Kraus F, Burges A, Czogalla B, Mayr D, Straub T, Klein C, Olsen JV, Mahner S, Trillsch F, Kessler M. iScience. 2025 Nov 10;28(12):113999.

Endometrial / related

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.

5. Murine & specialised bibliography

Murine intestinal, pancreatic, colon, lacrimal, thymic epithelial, xenograft, and other specialised organoid contexts.

Murine intestinal / small intestinal / large-intestinal-linked

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).
Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients. Buissant des Amorie JR, Betjes MA, Bernink JH, Hageman JH, Geurts VE, Begthel H, Laskaris D, Heinz MC, Jordens I, Vinck T, Houtekamer RM, Verlaan-Klink I, Brunner SR, van Rheenen J, Gloerich M, Clevers H, Tans SJ, van Zon JS, Snippert HJG. Nat Commun. 2025 Jul 22;16(1):6765.
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.
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.
Introducing the Stem Cell ASCL2 Reporter STAR into Intestinal Organoids. Heinz MC, Oost KC, Snippert HJG. STAR Protoc. 2020 Oct 8;1(3):100126.

Murine colon / murine normal colorectal / murine xenograft-linked

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.
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.
SPP1 is required for maintaining mesenchymal cell fate in pancreatic cancer. Li H, Lan L, Chen H, Zaw Thin M, Ps H, Nelson JK, Evans IM, Ruiz EJ, Cheng R, Tran L, Allen M, Ma J, Yi T, Wang C, He Y, Guppy N, Sadanandam A, Lin SZ, Zhang C, Behrens A. Nature. 2025 Dec;648(8092):203-209.

Murine lacrimal gland / thymic epithelial / specialised tissue models

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).
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.
Derivation of functional thymic epithelial organoid lines from adult murine thymus. Lim S, van Son JF, Wisma Eka Yanti NL, Andersson-Rolf A, Willemsen S, Korving J, Lee HG, Begthel H, Clevers H. Cell Rep. 2024 Apr 23;43(4):114019.

6. Additional mixed-context publications

A few publications sit across multiple contexts or appear under labels that are broader than the paper title itself.

Human liver ductal organoids: Single intact ordanoids electroporation by CUY650P1 electrodes.
Human hepatocyte organoids: Dissociated single cells cuvette electroporation.
Pancreatic cancer organoids – Murine xenografs. Label retained in line with the source PDF formatting.
Organoidderived neural progenitor cells(NPCs). Label retained in line with the source PDF formatting.

Summary

This bibliography page is intended as a dedicated reference companion to the SONIDEL organoid landing page, while expanding the publication list into a full browseable resource.

Discuss your organoid workflow with SONIDEL

If you would like help interpreting which of these publication contexts is closest to your own organoid workflow, SONIDEL can advise on a practical starting route, including whether your model is best approached as dissociated organoids, whole organoids, or an upstream stem/iPSC workflow.

Request: Help or Free NEPA21 Trial