Strategies for genetic manipulation of adult stem cell-derived organoids

Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice

(2021) Pengpeng Liu et al.   Nature Communications

CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank

(2020) Maarten H. Geurts et al.   Cell Stem Cell

Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches

(2020) Sungjin Min et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR–Cas9 precision genome editing

(2020) Benedetta Artegiani et al.   NATURE CELL BIOLOGY

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

(2020) Till Ringel et al.   Cell Stem Cell

Pooled In Vitro and In Vivo CRISPR-Cas9 Screening Identifies Tumor Suppressors in Human Colon Organoids

(2020) Birgitta E. Michels et al.   Cell Stem Cell

One for All: A Pooled Approach to Classify Functional Impacts of Multiple Mutations

(2020) Alexandre Jourdon et al.   Cell Stem Cell

Human organoids: model systems for human biology and medicine

(2020) Jihoon Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Lineage reversion drives WNT independence in intestinal cancer

(2020) Teng Han et al.   Cancer Discovery

Engineering a far-red light–activated split-Cas9 system for remote-controlled genome editing of internal organs and tumors

(2020) Yuanhuan Yu et al.   Science Advances

Phenotypic landscape of intestinal organoid regeneration

(2020) Ilya Lukonin et al.   NATURE

Prime editing for functional repair in patient-derived disease models

(2020) Imre F. Schene et al.   Nature Communications

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

(2020) Delilah Hendriks et al.   Nature Protocols

Human colon organoids reveal distinct physiologic and oncogenic Wnt responses

(2019) Birgitta E. Michels et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping

(2019) Helmuth Gehart et al.   CELL

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

(2019) Benedetta Artegiani et al.   Cell Stem Cell

Modeling breast cancer using CRISPR/Cas9-mediated engineering of human breast organoids

(2019) Johanna F Dekkers et al.   JNCI-Journal of the National Cancer Institute

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening

(2019) Minsuh Kim et al.   Nature Communications

Pancreatic cancer organoids recapitulate disease and allow personalized drug screening

(2019) Else Driehuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Pancreatic Tumor Organoids Reveal Loss of Stem Cell Niche Factor Dependence during Disease Progression

(2018) Takashi Seino et al.   Cell Stem Cell

Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium

(2018) Anna M. Nicholson et al.   Cell Stem Cell

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene

(2018) Koen C. Oost et al.   Cell Reports

Deriving functional human enteroendocrine cells from pluripotent stem cells

(2018) Katie L. Sinagoga et al.   DEVELOPMENT

A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells

(2018) Christopher A. Vakulskas et al.   NATURE MEDICINE

Modeling Human Digestive Diseases With CRISPR-Cas9–Modified Organoids

(2018) Masayuki Fujii et al.   GASTROENTEROLOGY

Engineered anti-CRISPR proteins for optogenetic control of CRISPR–Cas9

(2018) Felix Bubeck et al.   NATURE METHODS

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Visualization and targeting of LGR5+ human colon cancer stem cells

(2017) Mariko Shimokawa et al.   NATURE

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling

(2017) Claudia Y. Janda et al.   NATURE

One-step generation of conditional and reversible gene knockouts

(2017) Amanda Andersson-Rolf et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Human tissues in a dish: The research and ethical implications of organoid technology

(2017) Annelien L. Bredenoord et al.   SCIENCE

HMGA1 amplifies Wnt signalling and expands the intestinal stem cell compartment and Paneth cell niche

(2017) Lingling Xian et al.   Nature Communications

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Enhancing a Wnt-Telomere Feedback Loop Restores Intestinal Stem Cell Function in a Human Organotypic Model of Dyskeratosis Congenita

(2016) Dong-Hun Woo et al.   Cell Stem Cell

A Colorectal Tumor Organoid Library Demonstrates Progressive Loss of Niche Factor Requirements during Tumorigenesis

(2016) Masayuki Fujii et al.   Cell Stem Cell

Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome

(2016) Maximilian Müller et al.   MOLECULAR THERAPY

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9

(2016) Dominik Paquet et al.   NATURE

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

CRISPaint allows modular base-specific gene tagging using a ligase-4-dependent mechanism

(2016) Jonathan L. Schmid-Burgk et al.   Nature Communications

Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment

(2016) Ruben R. Bender et al.   PLoS Pathogens

Efficient Intracellular Delivery of Native Proteins

(2015) Diego S. D’Astolfo et al.   CELL

Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver

(2015) Meritxell Huch et al.   CELL

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

(2015) Sylvia F. Boj et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

Sequential cancer mutations in cultured human intestinal stem cells

(2015) Jarno Drost et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Small molecule–triggered Cas9 protein with improved genome-editing specificity

(2015) Kevin M Davis et al.   Nature Chemical Biology

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

(2015) Mami Matano et al.   NATURE MEDICINE

Efficient genetic engineering of human intestinal organoids using electroporation

(2015) Masayuki Fujii et al.   Nature Protocols

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids

(2015) Benjamin S. Freedman et al.   Nature Communications

Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures

(2014) Wouter R. Karthaus et al.   CELL

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

Single luminal epithelial progenitors can generate prostate organoids in culture

(2014) Chee Wai Chua et al.   NATURE CELL BIOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients

(2013) Gerald Schwank et al.   Cell Stem Cell

Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis

(2013) Meritxell Huch et al.   EMBO JOURNAL

In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration

(2013) Meritxell Huch et al.   NATURE

Efficient generation of lung and airway epithelial cells from human pluripotent stem cells

(2013) Sarah X L Huang et al.   NATURE BIOTECHNOLOGY

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

(2013) Xiaolei Yin et al.   NATURE METHODS

Generation of BAC Transgenic Epithelial Organoids

(2013) Gerald Schwank et al.   PLoS One

Extensive Methylation of Promoter Sequences Silences Lentiviral Transgene Expression During Stem Cell Differentiation In Vivo

(2012) Friederike Herbst et al.   MOLECULAR THERAPY

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Controlled gene expression in primary Lgr5 organoid cultures

(2011) Bon-Kyoung Koo et al.   NATURE METHODS

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche

(2009) Akifumi Ootani et al.   NATURE MEDICINE