CRISPR and RNAi Platforms for Genome- Wide Loss-of-Function Screens AACR April 21, 2015

Transcription

1 CRISPR and RNAi Platforms for Genome- Wide Loss-of-Function Screens AACR April 21, 2015 Paul Diehl, Ph.D. Director of Business Development Cellecta, Inc. Mountain View, CA

2 Cellecta Overview Founded: April 2006 Started Operations in July 2007 Headquarters: Mountain View, CA 12 SBIR Grants Network of collaborators (primarily cancer-related) Focuses on the development of flexible, scalable, and broadly parallel genetic screening assays to expedite the discovery and characterization of novel therapeutic targets for drug discovery.

3 Public Collaborations Khorashad JS, et al. (2015) "shrna library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance." Blood Jan 8 (125) DOI: /blood Natarajan V, et al., (2014) "Peptides genetically selected for NF-kB activation cooperate with oncogene Ras and model carcinogenic role of inflammation." PNAS 2014: v Leonova KI, et al., (2013) "p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs." Proc Natl Acad Sci U S A. Jan 2;110(1):E Neznanov N, et al., (2011) "Proteotoxic stress targeted therapy (PSTT): induction of protein misfolding enhances the antitumor effect of the proteasome inhibitor bortezomib." Oncotarget. Mar 2(3): In vivo Synthetic Lethality Screens to Identify Genetic Dependencies in Patient-Derived Tumor Models, Timothy Heffernan, Ph.D., Senior Associate Director, Target Discovery, Inst. for Applied Cancer Science, University of Texas, MD Anderson Cancer Center, Discovery on Target Conference Presentation, 2014 (Cambridge Healthtech). Nolan-Stevaux O, et al (2013) "Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment." PLoS One. Jun 26;8(6):e Print PMID: DECIPHER Open-Source Genome-wide RNAi Screening Libraries. The DECIPHER Project ( Moving beyond in vitro models and addressing the challenges of pooled RNAi screens in mouse xenografts, Donato Tedesco, Kyle Bonneau, Mikhail Makhanov, Debbie Deng, Paul Diehl, Peiqing Sun, and Alex Chenchik, AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA

4 Cellecta s Products/Services RNAi & CRISPR Loss-of-Function Screens RNAi shrna and CRISPR sgrna Pooled Libraries (Custom & Premade) Targeted Gene Knockdowns and Knockouts Assay Services Custom Lentiviral RNAi Knockdown and CRISPR Knockout Constructs Custom Lentiviral Expression and Reporter Constructs Knockdown, Knockout, Reporter, and cdna Cell Line Engineering NGS of RNAi and CRISPR Screens with Cellecta Libraries Complex Barcode Cell Tracking Libraries

5 shrna/sgrna Libraries

6 Loss of Function Genetic Analysis Finding and prioritizing drug targets Understanding disease progression and gene-disease associations Finding functional drivers in expression profiling data Analyzing signal transduction pathways Characterizing the mechanisms for compounds Uncovering synergistic gene interactions Identifying mechanisms and markers of drug resistance/sensitivity Research areas Oncology and Cancer Biology Infectious Diseases Inflammation Other diseases with cell-culture model systems

7 RNAi and CRISPR RNAi CRISPR

8 Screening Approaches Functional Assay Functional Assay / Selection Pooled Format Screening Advantages: Flexibility Any set of target genes, number of shrna, markers, promoters. Reproducibility Single assay, all variables consistent. Efficiency Faster and more economic, easy to screen 10s of shrna per gene.

9 sgrna/shrna Library Construction Oligo Pool Synthesis Agilent Array Synthesis Defined complex pools High yield long oligos Low mutation rate (< 0.5%) Cloning Optimized Cloning High complexity >99% representation Packaging Optimized Large Scale Maintains representation High Titer

10 shrna Vectors Standard Library Vector

11 Library QC by NGS 27K Plasmid shrna Library ~90% inserts within 10-fold abundance range (i.e. narrow distribution) ~95% of shrna constructs without mutations/deletions ~98% shrna insert rate Poor Quality

12 Pooled shrna/sgrna Libraries Custom Libraries (2-3 months: $25-$50K depending on size) Just give us a gene list and we Design shrna/sgrna sequences Synthesize oligos Clone our optimized vectors, customized vectors, or customer s own vector QC by NGS sequencing and full analysis of select clones Library packaging available Premade Libraries Genome-Wide (hgw) shrna Library--Targets 19,276 Human Genes 3 Modules, each targeting approximately 6,500 genes Each gene is targeted by 8 hairpins 55,000 hairpins per module CRISPR Genome-Wide sgrna Library--Targets 19,276 human Genes (in development) Each gene targeted by 8 sgrna 55,000 hairpins per module (first module complete)

13 Loss of Function Genetic Screens

14 Cellecta Loss of Function Screening Platform sgrna/

15 Types of Screens Rescue/Survival Screens (Positive Selection): Find genes required to produce a response to added factors or compound; for example, genes necessary for trigging apoptosis or cell death in response to FAS, PUMA or other effectors. Viability/Dropout Screens (Negative Selection): Identify essential genes in a specific population of cells (e.g., prostate, blood, mammary cancer cells). Selected Populations (e.g., FACS): Look for modulators of NF-κB, p53, c-myc, HSF-1, HIF-1α using fluorescent reporter cell line, or cells expressing specific Abdetectable marker, such as specific receptors.

16 Viability Screen for Blood Neoplasia K562 Cells Cellecta Human 27K Library Targeting Signaling Pathway Genes

17 Viability Hits Associated with K562 Cells * * * Overlap with previous study: Luo B, et al. Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A Dec 23;105(51):

18 Abstract BCR-ABL1 kinase domain mutations are detected in 30-60% of patients who develop resistance to tyrosine kinase inhibitors (TKIs) such as imatinib. However, the underlying mechanism(s) of resistance in the remaining patients are not known. To identify BCR-ABL1-independent mechanisms of resistance to TKIs, we used K562 cells that were adapted for long-term growth in 1 µm imatinib (K562-R). These cells lack BCR- ABL1 kinase domain mutations and survive despite continued suppression of BCR-ABL1 kinase activity. To screen for novel genes associated with BCR-ABL1-independent resistance, parental K562 and K562-R cells were lentivirally infected with a pooled shrna library containing 27,000 shrnas targeting 5,000 genes with known roles in cell signaling (Cellecta, Human Module 1).

19 Found BRG1/SMARCA4 mutant cancer cells are highly sensitive to BRM/ SMARCA2 depletion.

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21 Citations of Cellecta s RNAi Libraries Wagenaar, T, R, et al. (2014), Identification of the endosomal sorting complex required for transport-i (ESCRT-I) as an important modulator of anti-mir uptake by cancer cells. Nucleic Acids Res Jan 30;43(2): doi: /nar/gku1367. Epub 2014 Dec 30. An Integrated Genomic and Chemical Screening Platform for Oncology Target Discovery, Serena Silver, Ph.D., Principal Research Investigator, Sanofi Oncology Target Discovery, Discovery on Target Conference Presentation, 2012 (Cambridge Healthtech) Mele DA, et al. (2013). "BET bromodomain inhibition suppresses TH17-mediated pathology." J Exp Med. Oct 21;210(11): Hoffman GR, et al (2014) "Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers." PNAS. PMID: Genomic Platforms to Generate Unbiased Responder and Treatment Hypotheses for Oncology Translational Research, Jing Li, Ph.D., Director of Genomics Screening, Discovery and Pre-clinical Science, Merck Research Laboratories, Discovery on Target Conference Presentation, 2012 (Cambridge Healthtech) Wolf J, et al. (2013) "An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation." Oncogene. December 2013; doi: /onc Wolf J, et al. (2013) "A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype." Breast Cancer Research. 15:R109. Fredebohm J, et al. (2013) "Depletion of RAD17 sensitizes pancreatic cancer cells to gemcitabine." J Cell Sci. Aug 1;126(Pt 15): Amy M S, et al, (2014) Casp8p41 generated by HIV protease kills CD4 T cells through direct Bak activation. JCB Sept 22 (206): Christiana S K, et al. (2015), Oncogenic signaling in amphiregulin and EGFR-expressing PTEN-null human breast cancer. Feb (9): Satish S K, et al. (2014), Vulnerability of Glioblastoma Cells to Catastrophic Vacuolization and Death Induced by a Small Molecule. Cell Apr 10 (175):

22 Development of CRISPR Libraries

23 Published CRISPR Screens

24 Site-Specific Gene Deletion with CRISPR Clustered Regularly Interspaced Short Palindromic Repeats genomic elements found in bacteria defense against invading viruses Offers Convenient Genome Editing Tool Elements of the CRISPR System Single-guide RNA (sgrna) - 20 base RNA sequence - Targets gene Cas9 Protein Figure from Case Transgenic and Targeting Core Facility, Case Western Reserve (

25 Single Vector CRISPR Construct Cas9 and sgrna in Same Vector No Co-Transduction prsgc1-u6-sg-cmv-cas9-2a-puro 11.5 kb

26 GFP-Expressing HEK293 Cells 7 days post-transduction with single CRISPR plasmid expressing sgrna to GFP no sgrna GFP sgrna #D1 GFP sgrna #C3

27 % Cells with Knocked Out GFP Day 9 Day 14

28 Effect of Cas9 Expression Level on KO CMV UbiC 9 days

29 CRISPR Vectors AmpR promoter prsgc1-u6-sg-cmv-cas9-2a-puro 11.5 kb prsg16-u6-sg-ubic-tagrfp-2a-puro 8.0 kb pr-cmv-cas9-2a-hygro 11.6 kb

30 Titers with Cas9 Lentivirus 2-vector system 1-vector system

31 CRISPR 2-Vector Systems pr-cas9-hygro + prsg16-sgrna-puro

32 1 vs. 2 Vector CRISPR Knockout

33 CRISPR KO v. Cas9 Level

34 Different CRISPR Designs

35 Pooled Loss of Function Screens: CRISPR vs. RNAi Screen

36 CRISPR/shRNA Screen Patient-Derived (PDx) CML Cells (K-CML) * courtesy of collaborators at Roswell Park Cancer Institute Transduced w/ Cas9-hyg, MOI = 2 Cas9-expressing Derivative Cells Grow Cells to 40M, Transduce with 20M TU Library (ca. 400 cells / construct) Libraries: 3 days Puro Selection Grow and Harvest 2 weeks 3 weeks 4 weeks 55K shrna hgw Library Module 1 Targets ca. 6,500 human genes 8 shrna/target 55K CRISPR Genome Library Module 1 Targets ca. 6,500 human genes 8 sgrna/target

37 Screen Results

38 Analysis of the Controls Depletion averages for negative (non-targeting) and positive (lethal) controls in the library. shrna seem to deplete more strongly but the SD is much broader.

39 Difference Between Pos v. Neg Controls Strictly Standardized Mean Difference (quantifies difference between pos/neg controls) shrna response more rapid but noise increases at later times sgrna longer to reach performance peak but signal is more consistent Genetic drift doesn t seem to be as much an issue with sgrna

40 Frequency of shrna and grna Hits

41 Number of grna v. shrna Hits per Gene About 35% of target genes identified by a single shrna hit (~ 2,300 shrnas) compared to about only 5% of genes (~320 grnas). Roughly same numbers of target genes were identified by multiple hits in CRISPR and RNAi screens.

42 Overlap of RNAi and CRISPR

43 Exclusive Hits of RNAi or CRISPR CRISPR CML-R CML-P ATP6V0B ATP6V0B CCNH CHORDC1 DHDDS DHFR DHFR ERCC2 ERCC2 FARSA FARSA FARSB NARFL NARFL PGAM1 PGAM1 RNMT SCYL1 SCYL1 TRMT112 TRMT112 YARS2 Strong score with CRISPR, none with shrna RNAi CML-R CML-P MTAP OTOGL TAF1L UBC UBC Strong score with shrna, none with CRISPR

44 ~47% Overlap between CRISPR & RNAi a= 0.01 & z-score=2.58

45 DNMT1 (only CRISPR) BCR ABL1 CCND3 MTOR PRPF31 HMGA2 BCL2 AKT1 (CRISPR and RNAi) (only RNAi)

46 Cellecta CRISPR Products/Services CRISPR/shRNA Screens Full Screening in mammalian cell system of choice Transduction, selection, NGS, Deconvolution è Data Pooled CRISPR Libraries Customer just needs to provide the target gene list CRISPR Genome-Wide Library CRISPR Knockout Constructs Clone customer-provided sgrna or design and provide several CRISPR constructs to gene target Custom Knockout Cell Lines Knockout endogenous genes in any common cell line Customer just provides information on target gene and cell line Cellecta returns two clonal lines with knockout verified by genomic sequencing

47 Multiplex-PCR/NGS Assays that Profile Genetic Markers in Cancer Cells

48 Cancer Profiling Assays Multiplex PCR/NGS-based assays for molecular profiling of key gene transcript levels, mutations and rearrangements in human tumor and PDx samples. Targeting key genes associated with prognoses & sensitivities Core panel of couple hundred markers Additional modules focusing on blood, immune markers, etc. Target set of ca genes with optimized primers in final panel Include expression & mutation analysis Provide internal calibration standards for background correction Multiplex PCR designed specifically for human (not mouse) genes

49 NGS Expression Profiling

50 Thank You! Paul Diehl Director of Business Development Tel: Cellecta, Inc. 320 Logue Ave. Mountain View, CA, USA