Bidirectional epigenetic editing reveals hierarchies in gene regulation

CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants.

An evolved AAV variant enables efficient genetic engineering of murine T cells

Precise targeting of large transgenes to T cells using homology-directed repair has been transformative for adoptive cell therapies and T cell biology. Delivery of DNA templates via adeno-associated virus (AAV) has greatly improved knockin efficiencies, but the tropism of current AAV serotypes restricts their use to human T cells employed in immunodeficient mouse models. To enable targeted knockins in murine T cells, we evolved Ark313, a synthetic AAV that exhibits high transduction efficiency in murine T cells. We performed a genome-wide knockout screen and identified QA2 as an essential factor for Ark313 infection. We demonstrate that Ark313 can be used for nucleofection-free DNA delivery, CRISPR-Cas9-mediated knockouts, and targeted integration of large transgenes. Ark313 enables preclinical modeling of Trac-targeted CAR-T and transgenic TCR-T cells in immunocompetent models. Efficient gene targeting in murine T cells holds great potential for improved cell therapies and opens avenues in experimental T cell immunology.

SCFFBXW7 regulates G2-M progression through control of CCNL1 ubiquitination

FBXW7, which encodes a substrate-specific receptor of an SCF E3 ligase complex, is a frequently mutated human tumor suppressor gene known to regulate the post-translational stability of various proteins involved in cellular proliferation. Here, using genome-wide CRISPR screens, we report a novel synthetic lethal genetic interaction between FBXW7 and CCNL1 and describe CCNL1 as a new substrate of the SCF-FBXW7 E3 ligase. Further analysis showed that the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle since defective CCNL1 accumulation, resulting from FBXW7 mutation, leads to shorter mitotic time. Cells harboring FBXW7 loss-of-function mutations are hypersensitive to treatment with a CDK11 inhibitor, highlighting a genetic vulnerability that could be leveraged for cancer treatment.

CRISPRi and KO screens reveal integrated cis- and trans-regulation of the CD28, CTLA4, and ICOS locus in primary human T cells

Costimulation is essential for complete T cell activation, requiring the coordinated expression of various surface proteins including those encoded by CD28 family members CD28, CTLA4, and ICOS. Interestingly, these three genes lie adjacently in a topologically-associating domain (TAD) and are believed to have arisen through duplications of CD28, though they have evolved opposing functions and exhibit expression differences across cell states and T cell subsets. We hypothesized that distinct cis- and trans-regulatory circuits emerged to uniquely govern the expression of each gene. Therefore, we tiled CRISPR interference (CRISPRi) across the 1.44Mb TAD in primary human conventional (Tconv) and regulatory T (Treg) cells to functionally profile cis-regulatory elements (CREs) controlling expression of CD28, CTLA4, and ICOS. We find that inhibiting the transcriptional start site of one gene (but not gene KO) enhances the expression of an adjacent gene, potentially due to redirection of shared CREs to the un-inhibited promoter. Moreover, we find distinct CREs responsible for constitutive expression of CTLA4 in Treg cells but stimulation-responsiveness in Tconv cells. We also find evidence of a single CRE that negatively regulates CD28 at baseline but positively regulates CTLA4 upon restimulation. Lastly, we characterize mechanisms of CRE control by identifying upstream regulators of target genes via CRISPR knockout screening. Our work nominates ZNF217, a zinc finger protein with no known function in human T cells, as a novel negative regulator altering chromatin accessibility in the locus. Here, we present a framework for functional characterization of regulatory modules controlling loci of interest in primary human CD4+ T cells.

CM is supported by NIAID F30 AI157167-01 and is a UCSF ImmunoX Computational Immunology Fellow. ZS is supported by the Parker Institute for Cancer Immunology scholarship. RS was supported by fellowships of the Austrian Exchange Service and the Austrian Society of Laboratory Medicine. C.J.Y. and AM are Chan Zuckerberg Biohub Investigators and members of the PICI. C.J.Y. is further supported by the National Institutes of Health (NIH) grant nos. R01AR071522, R01AI136972 and R01HG011239.  AM is supported by National Institute of Diabetes and Digestive and Kidney Diseases DP3DK111914-01 (AM) Simons Foundation (AM) Burroughs Wellcome Fund, Career Award for Medical Scientists (AM) The Cancer Research Institute (CRI) Lloyd J. Old STAR grant (AM) Parker Institute for Cancer Immunotherapy, PICI (AM) Innovative Genomics Institute (IGI) National Institutes of Health grant P30 DK063720 (Parnassus Flow Cytometry Core, AM) National Institutes of Health grant S10 1S10OD021822-01 (Parnassus Flow Cytometry Core, AM) Investigator at the Chan Zuckerberg Biohub (AM) Gifts from Brook Byers, Barbara Bakar, Karen Jordan, Elena Radutzky

CRISPR activation and interference screens decode stimulation responses in primary human T cells

Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin-2 (IL-2) and interferon-γ (IFN-γ) production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA sequencing enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. These screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells

Glioblastoma therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells (GSCs) to interrogate function of the coding genome, we identify actionable pathways responsible for growth, which reveal the gene-essential circuitry of GBM stemness and proliferation. In particular, we characterize members of the SOX transcription factor family, SOCS3, USP8, and DOT1L, and protein ufmylation as important for GSC growth. Additionally, we reveal mechanisms of temozolomide resistance that could lead to combination strategies. By reaching beyond static genome analysis of bulk tumors, with a genome-wide functional approach, we reveal genetic dependencies within a broad range of biological processes to provide increased understanding of GBM growth and treatment resistance.

IPO11 mediates βcatenin nuclear import in a subset of colorectal cancers

Activation of Wnt signaling entails βcatenin protein stabilization and translocation to the nucleus to regulate context-specific transcriptional programs. The majority of colorectal cancers (CRCs) initiate following APC mutations, resulting in Wnt ligand-independent stabilization and nuclear accumulation of βcatenin. The mechanisms underlying βcatenin nucleocytoplasmic shuttling remain incompletely defined. Using a novel, positive selection, functional genomic strategy, DEADPOOL, we performed a genome-wide CRISPR screen and identified IPO11 as a required factor for βcatenin-mediated transcription in APC mutant CRC cells. IPO11 (Importin-11) is a nuclear import protein that shuttles cargo from the cytoplasm to the nucleus. IPO11-/- cells exhibit reduced nuclear βcatenin protein levels and decreased βcatenin target gene activation, suggesting IPO11 facilitates βcatenin nuclear import. IPO11 knockout decreased colony formation of CRC cell lines and decreased proliferation of patient-derived CRC organoids. Our findings uncover a novel nuclear import mechanism for βcatenin in cells with high Wnt activity.

Tailored tetravalent antibodies potently and specifically activate Wnt/Frizzled pathways in cells, organoids and mice

Secreted Wnt proteins regulate development and adult tissue homeostasis by binding and activating cell-surface Frizzled receptors and co-receptors including LRP5/6. The hydrophobicity of Wnt proteins has complicated their purification and limited their use in basic research and as therapeutics. We describe modular tetravalent antibodies that can recruit Frizzled and LRP5/6 in a manner that phenocopies the activities of Wnts both in vitro and in vivo. The modular nature of these synthetic Frizzled and LRP5/6 Agonists, called FLAgs, enables tailored engineering of specificity for one, two or multiple members of the Frizzled family. We show that FLAgs underlie differentiation of pluripotent stem cells, sustain organoid growth, and activate stem cells in vivo. Activation of Wnt signaling circuits with tailored FLAgs will enable precise delineation of functional outcomes directed by distinct receptor combinations and could provide a new class of therapeutics to unlock the promise of regenerative medicine.

A synthetic anti-Frizzled antibody engineered for broadened specificity exhibits enhanced anti-tumor properties

Secreted Wnt ligands play a major role in the development and progression of many cancers by modulating signaling through cell-surface Frizzled receptors (FZDs). In order to achieve maximal effect on Wnt signaling by targeting the cell surface, we developed a synthetic antibody targeting six of the 10 human FZDs. We first identified an anti-FZD antagonist antibody (F2) with a specificity profile matching that of OMP-18R5, a monoclonal antibody that inhibits growth of many cancers by targeting FZD7, FZD1, FZD2, FZD5 and FZD8. We then used combinatorial antibody engineering by phage display to develop a variant antibody F2.A with specificity broadened to include FZD4. We confirmed that F2.A blocked binding of Wnt ligands, but not binding of Norrin, a ligand that also activates FZD4. Importantly, F2.A proved to be much more efficacious than either OMP-18R5 or F2 in inhibiting the growth of multiple RNF43-mutant pancreatic ductal adenocarcinoma cell lines, including patient-derived cells.

Wnt signaling in development and tissue homeostasis

The Wnt-β-catenin signaling pathway is an evolutionarily conserved cell-cell communication system that is important for stem cell renewal, cell proliferation and cell differentiation both during embryogenesis and during adult tissue homeostasis. Genetic or epigenetic events leading to hypo- or hyper-activation of the Wnt-β-catenin signaling cascade have also been associated with human diseases such as cancer. Understanding how this pathway functions is thus integral for developing therapies to treat diseases or for regenerative medicine approaches. Here, and in the accompanying poster, we provide an overview of Wnt-β-catenin signaling and briefly highlight its key functions during development and adult tissue homeostasis.

Essential role of the Dishevelled DEP domain in a Wnt-dependent human-cell-based complementation assay

Dishevelled (DVL) assembles Wnt signalosomes through dynamic head-to-tail polymerisation by means of its DIX domain. It thus transduces Wnt signals to cytoplasmic effectors including β-catenin, to control cell fates during normal development, tissue homeostasis and also in cancer. To date, most functional studies of Dishevelled relied on its Wnt-independent signalling activity resulting from overexpression, which is sufficient to trigger polymerisation, bypassing the requirement for Wnt signals. Here, we generate a human cell line devoid of endogenous Dishevelled (DVL1- DVL3), which lacks Wnt signal transduction to β-catenin. However, Wnt responses can be restored by DVL2 stably re-expressed at near-endogenous levels. Using this assay to test mutant DVL2, we show that its DEP domain is essential, whereas its PDZ domain is dispensable, for signalling to β-catenin. Our results imply two mutually exclusive functions of the DEP domain in Wnt signal transduction - binding to Frizzled to recruit Dishevelled to the receptor complex, and dimerising to cross-link DIX domain polymers for signalosome assembly. Our assay avoids the caveats associated with overexpressing Dishevelled, and provides a powerful tool for rigorous functional tests of this pivotal human signalling protein.

Dishevelled is a NEK2 kinase substrate controlling dynamics of centrosomal linker proteins

Dishevelled (DVL) is a key scaffolding protein and a branching point in Wnt signaling pathways. Here, we present conclusive evidence that DVL regulates the centrosomal cycle. We demonstrate that DVL dishevelled and axin (DIX) domain, but not DIX domain-mediated multimerization, is essential for DVL's centrosomal localization. DVL accumulates during the cell cycle and associates with NIMA-related kinase 2 (NEK2), which is able to phosphorylate DVL at a multitude of residues, as detected by a set of novel phospho-specific antibodies. This creates interfaces for efficient binding to CDK5 regulatory subunit-associated protein 2 (CDK5RAP2) and centrosomal Nek2-associated protein 1 (C-NAP1), two proteins of the centrosomal linker. Displacement of DVL from the centrosome and its release into the cytoplasm on NEK2 phosphorylation is coupled to the removal of linker proteins, an event necessary for centrosomal separation and proper formation of the mitotic spindle. Lack of DVL prevents NEK2-controlled dissolution of loose centrosomal linker and subsequent centrosomal separation. Increased DVL levels, in contrast, sequester centrosomal NEK2 and mimic monopolar spindle defects induced by a dominant negative version of this kinase. Our study thus uncovers molecular crosstalk between centrosome and Wnt signaling.

Abstract IA13: Inhibiting the Wnt pathway with selective anti-Frizzled synthetic antibodies

Secreted Wnt glycoproteins regulate intracellular signaling pathways important for embryonic development and adult tissue homeostasis. Misregulation of Wnt signalling is frequent in human cancers. Wnt ligands are recognized at the surface of cells by various receptor complexes that are differentially expressed and determine context-dependent cellular responses. In humans, 16 Wnt ligands interact directly with 10 Frizzled seven transmembrane proteins through their extracellular cysteine rich domain (CRD). Wnts also interact with various co-receptors, such as LRP5/6, ROR1/2, RYK, PTK7, which engage different downstream signaling pathways. While genetic analysis of mouse knockouts has revealed specific roles for different Wnt receptors and co-receptors during embryonic development, relatively little is known about their respective functions during adult tissue homeostasis or in the initiation and progression of human diseases such as cancer. There is a paucity of reagents allowing the selective and temporal pharmacological inhibition of Wnt receptors. We are employing phage-display technology to identify high affinity synthetic blocking monoclonal antibodies (mAbs) against all human Wnt receptors. To date we have isolated a collection of anti-receptor antibodies exhibiting unique selectivity and functionality profiles. Our lead anti-Frizzled mAbs targeting a subset of Frizzled proteins inhibit Wnt-promoted activation of the TopFlash reporter with low nanomolar potency. These mAbs also exhibit dose dependent anti-proliferative efficacies against various pancreatic cancer cell lines grown in vitro and as xenografts in mice.

These reagents will be useful to probe the function of specific Wnt receptors in tissue homeostasis and human diseases and will lead to novel therapeutic agents for their treatment.

Our lab is also employing whole genome CRISPR screening approach to identify genotype specific vulnerabilities in cancer cells. These efforts have identified specific Frizzled important for cancer cells proliferation and is guiding our antibody development program.

Citation Format: Zachary Steinhart, Traver Hart, Sachdev Sidhu, Jason Moffat, Stephane Angers. Inhibiting the Wnt pathway with selective anti-Frizzled synthetic antibodies. [abstract]. In: Proceedings of the AACR Special Conference: Developmental Biology and Cancer; Nov 30-Dec 3, 2015; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(4_Suppl):Abstract nr IA13.

Abstract PR03: High-resolution detection of fitness genes and genotype-specific cancer vulnerabilities with CRISPR-Cas9 screens

Genetic knockouts are a fundamental tool for elucidating gene function in model organisms and hold great potential for finding therapeutic targets for diseases such as cancer. The advance that pooled CRISPR-Cas9 library technology brings to human genetics sets the stage for identifying cellular fitness genes which operate either globally or specifically within a particular genetic background or environmental context. To extend the catalogue of human core and context-dependent fitness genes, we have developed the TKO (Toronto KnockOut) library, a second-generation gRNA library of 176,500 guides targeting 17,661 human protein coding genes. We used the library to screen five human cell lines, representing a cross-section of wild type and cancer tissues, to identify genes whose knockouts induced significant fitness defects. We consistently discover fivefold more fitness genes than were previously observed using systematic RNA interference, including many genes at moderate expression levels that are largely refractory to RNAi methods. We expand the known set of human core fitness genes more than fourfold to 1,580 genes, and identify dozens of essential protein complexes, both known and novel, whose heterozygous copy loss in chromosomally unstable cancers may induce a therapeutic window. We further characterize novel fitness genes of unknown function and find that they all likely exist in protein complexes with other essential genes. TKO screens accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. We also identified a surprising and specific dependency on mitochondrial activity, which strongly supports the idea that oxidative phosphorylation dependency - a clear exception to the Warburg effect - is a targetable weakness of some tumors. Our findings demonstrate that the CRISPR-Cas9 system fundamentally alters the landscape for systematic genetics in human cells through rigorous identification of cell line essential genes, affording a high-resolution view of the genetic vulnerabilities of a cell that may represent therapeutic opportunities in cancer and that might conceivably contribute to cell plasticity and tumor progression.

Citation Format: Traver Hart, Megha Chandrashekhar, Michael Aregger, Zachary Steinhart, Kevin R. Brown, Graham Macleod, Monika Mis, Michal Zimmermann, Amelie Fradet-Turcotte, Song Sun, Peter Driks, Sachdev Sidhu, Frederick P. Roth, Olivia S. Rissland, Daniel Durocher, Stephane Angers, Jason Moffat. High-resolution detection of fitness genes and genotype-specific cancer vulnerabilities with CRISPR-Cas9 screens. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr PR03.

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

The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.

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

The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.