Discovering and validating cancer genetic dependencies: approaches and pitfalls

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities

(2020) Kyuho Han et al.   NATURE

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

Cas9 activates the p53 pathway and selects for p53-inactivating mutations

(2020) Oana M. Enache et al.   NATURE GENETICS

SpCas9-expression by tumor cells can cause T cell-dependent tumor rejection in immunocompetent mice

(2019) Reham Ajina et al.   OncoImmunology

Novel mutations in the kinase domain of BCR-ABL gene causing imatinib resistance in chronic myeloid leukemia patients

(2019) Chodimella Chandrasekhar et al.   Scientific Reports

Target identification reveals lanosterol synthase as a vulnerability in glioma

(2019) Richard E. Phillips et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective pharmacological inhibitors of HDAC6 reveal biochemical activity but functional tolerance in cancer models

(2019) Yves Depetter et al.   INTERNATIONAL JOURNAL OF CANCER

Genetic compensation triggered by mutant mRNA degradation

(2019) Mohamed A. El-Brolosy et al.   NATURE

Lethal clues to cancer-cell vulnerability

(2019) Felix Y. Feng et al.   NATURE

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Application of Cancer Organoid Model for Drug Screening and Personalized Therapy

(2019) Jumpei Kondo et al.   Cells

VISAGE Reveals a Targetable Mitotic Spindle Vulnerability in Cancer Cells

(2019) Jesse C. Patterson et al.   Cell Systems

Reply to “CRISPR screens are feasible in TP53 wild‐type cells”

(2019) Emma Haapaniemi et al.   Molecular Systems Biology

CRISPR screens are feasible in TP 53 wild‐type cells

(2019) Kevin R Brown et al.   Molecular Systems Biology

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

(2019) Ann Lin et al.   Science Translational Medicine

Biological plasticity rescues target activity in CRISPR knock outs

(2019) Arne H. Smits et al.   NATURE METHODS

Genome-scale CRISPR screens are efficient in non-homologous end-joining deficient cells

(2019) Joana Ferreira da Silva et al.   Scientific Reports

Estimation of clinical trial success rates and related parameters

(2018) Chi Heem Wong et al.   BIOSTATISTICS

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity

(2018) Norman Sachs et al.   CELL

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Humanized mice in studying efficacy and mechanisms of PD-1-targeted cancer immunotherapy

(2018) Minan Wang et al.   FASEB JOURNAL

Protein targeting chimeric molecules specific for bromodomain and extra-terminal motif family proteins are active against pre-clinical models of multiple myeloma

(2018) Xiaohui Zhang et al.   LEUKEMIA

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

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation

(2018) Michael J. Thomenius et al.   PLoS One

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes

(2018) Jasper Edgar Neggers et al.   Nature Communications

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

Challenges in validating candidate therapeutic targets in cancer

(2018) Jeffrey Settleman et al.   eLife

MELK expression correlates with tumor mitotic activity but is not required for cancer growth

(2018) Christopher J Giuliano et al.   eLife

Reproducibility vs. Replicability: A Brief History of a Confused Terminology

(2018) Hans E. Plesser   Frontiers in Neuroinformatics

Transgenic Mouse Models in Cancer Research

(2018) Ursa Lampreht Tratar et al.   Frontiers in Oncology

CRISPR/Cas9-mediated genome editing induces exon skipping by complete or stochastic altering splicing in the migratory locust

(2018) Dafeng Chen et al.   BMC BIOTECHNOLOGY

How selective are pharmacological inhibitors of cell cycle-regulating cyclin-dependent kinases?

(2018) Radek Jorda et al.   JOURNAL OF MEDICINAL CHEMISTRY

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Cas9 immunity creates challenges for CRISPR gene editing therapies

(2018) Julie M. Crudele et al.   Nature Communications

CRISPR/Cas9-mediated genome editing induces gene knockdown by altering the pre-mRNA splicing in mice

(2018) Ji-Xin Tang et al.   BMC BIOTECHNOLOGY

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response

(2018) Karol Szlachta et al.   Nature Communications

CD95/Fas ligand mRNA is toxic to cells

(2018) Will Putzbach et al.   eLife

Patient-derived organoids: a promising model for personalized cancer treatment

(2018) Huayu Yang et al.   Gastroenterology Report

Patient-derived xenografts undergo mouse-specific tumor evolution

(2017) Uri Ben-David et al.   NATURE GENETICS

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis

(2017) Jonathan J. Ipsaro et al.   PLoS One

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

(2017) Joseph Rosenbluh et al.   Nature Communications

Development of a 3D angiogenesis model to study tumour – endothelial cell interactions and the effects of anti-angiogenic drugs

(2017) Arno Amann et al.   Scientific Reports

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

(2017) William Putzbach et al.   eLife

Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine

(2016) Maximilian W. Popp et al.   CELL

Drugging the addict: non‐oncogene addiction as a target for cancer therapy

(2016) Remco Nagel et al.   EMBO REPORTS

Potent and Selective Inhibitors of MTH1 Probe Its Role in Cancer Cell Survival

(2016) Jason G. Kettle et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

(2016) Bernd Zetsche et al.   NATURE BIOTECHNOLOGY

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

(2016) D. M. Munoz et al.   Cancer Discovery

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening

(2016) Carla S Verissimo et al.   eLife

An Inducible System for Rapid Degradation of Specific Cellular Proteins Using Proteasome Adaptors

(2016) Shameika R. Wilmington et al.   PLoS One

Naturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance

(2015) M. D. Gurden et al.   CANCER RESEARCH

Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes

(2015) Victoria Vu et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

(2015) Sylvia F. Boj et al.   CELL

Preclinical Mouse Cancer Models: A Maze of Opportunities and Challenges

(2015) Chi-Ping Day et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics

(2015) A. Goodspeed et al.   MOLECULAR CANCER RESEARCH

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

(2015) Michael Boettcher et al.   MOLECULAR CELL

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

Catalytic in vivo protein knockdown by small-molecule PROTACs

(2015) Daniel P Bondeson et al.   Nature Chemical Biology

The promise and peril of chemical probes

(2015) Cheryl H Arrowsmith et al.   Nature Chemical Biology

The history and future of targeting cyclin-dependent kinases in cancer therapy

(2015) Uzma Asghar et al.   NATURE REVIEWS DRUG DISCOVERY

An analysis of the attrition of drug candidates from four major pharmaceutical companies

(2015) Michael J. Waring et al.   NATURE REVIEWS DRUG DISCOVERY

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comparison of 2D- and 3D-culture models as drug-testing platforms in breast cancer

(2015) YOSHINORI IMAMURA et al.   ONCOLOGY REPORTS

The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects

(2015) Piotr J. Kamola et al.   PLoS Computational Biology

Modeling human carcinomas: Physiologically relevant 3D models to improve anti-cancer drug development

(2014) Christine Unger et al.   ADVANCED DRUG DELIVERY REVIEWS

The crystal structure of MPK38 in complex with OTSSP167, an orally administrative MELK selective inhibitor

(2014) Yong-Soon Cho et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Systemic therapy for early-stage HER2-positive breast cancers: Time for a less-is-more approach?

(2014) Elisavet Paplomata et al.   CANCER

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

A Computational Algorithm to Predict shRNA Potency

(2014) Simon R.V. Knott et al.   MOLECULAR CELL

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool

(2014) Helge Gad et al.   NATURE

Clinical development success rates for investigational drugs

(2014) Michael Hay et al.   NATURE BIOTECHNOLOGY

DrugTargetSeqR: a genomics- and CRISPR-Cas9–based method to analyze drug targets

(2014) Corynn Kasap et al.   Nature Chemical Biology

Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research

(2014) M. Hidalgo et al.   Cancer Discovery

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma

(2012) Lee A.D. Cooper et al.   AMERICAN JOURNAL OF PATHOLOGY

Improved survival in chronic myeloid leukemia since the introduction of imatinib therapy: a single-institution historical experience

(2012) H. Kantarjian et al.   BLOOD

Trapping of PARP1 and PARP2 by Clinical PARP Inhibitors

(2012) J. Murai et al.   CANCER RESEARCH

Oncogene addiction

(2012) Jeffrey Settleman   CURRENT BIOLOGY

Targeting the EGFR signaling pathway in cancer therapy

(2012) Parthasarathy Seshacharyulu et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Discovery of small molecule cancer drugs: Successes, challenges and opportunities

(2012) Swen Hoelder et al.   Molecular Oncology

Using transcriptome sequencing to identify mechanisms of drug action and resistance

(2012) Sarah A Wacker et al.   Nature Chemical Biology

A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens

(2012) Frederic D Sigoillot et al.   NATURE METHODS

C911: A Bench-Level Control for Sequence Specific siRNA Off-Target Effects

(2012) Eugen Buehler et al.   PLoS One

STK33 kinase inhibitor BRD-8899 has no effect on KRAS-dependent cancer cell viability

(2012) T. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Potent and Selective Quinoxalinone-Based STK33 Inhibitor Does Not Show Synthetic Lethality in KRAS-Dependent Cells

(2012) Michel Weïwer et al.   ACS Medicinal Chemistry Letters

STK33 Kinase Activity Is Nonessential in KRAS-Dependent Cancer Cells

(2011) C. Babij et al.   CANCER RESEARCH

Vemurafenib and BRAF Inhibition: A New Class of Treatment for Metastatic Melanoma

(2011) J. J. Luke et al.   CLINICAL CANCER RESEARCH

Redefining the relevance of established cancer cell lines to the study of mechanisms of clinical anti-cancer drug resistance

(2011) J.-P. Gillet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing the Probes: Fitness Factors For Small Molecule Tools

(2010) Paul Workman et al.   CHEMISTRY & BIOLOGY

Collaboration and competition between DNA double-strand break repair pathways

(2010) Elizabeth M. Kass et al.   FEBS LETTERS

The art of the chemical probe

(2010) Stephen V Frye   Nature Chemical Biology

Synthetic Lethal Interaction between Oncogenic KRAS Dependency and STK33 Suppression in Human Cancer Cells

(2009) Claudia Scholl et al.   CELL

Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction

(2009) Ji Luo et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

(2009) Aly A Khan et al.   NATURE BIOTECHNOLOGY

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

(2009) Aimee L. Jackson et al.   NATURE REVIEWS DRUG DISCOVERY

Loss-of-function genetic screens as a tool to improve the diagnosis and treatment of cancer

(2009) J Mullenders et al.   ONCOGENE

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening

(2008) J. M. Silva et al.   SCIENCE