PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues

CRISPR/Cas9 functional genomic screens have emerged as essential tools in drug target discovery. However, the sensitivity of available genome-wide CRISPR libraries is impaired by guides which inefficiently abrogate gene function. While Cas9 cleavage efficiency optimization and essential domain targeting have been developed as independent guide design rationales, no library has yet combined these into a single cohesive strategy to knock out gene function. Here, in a massive reanalysis of CRISPR tiling data using the most comprehensive feature database assembled, we determine which features of guides and their targets best predict activity and how to best combine them into a single guide design algorithm. We present the ProteIN ConsERvation (PINCER) genome-wide CRISPR library, which for the first time combines enzymatic efficiency optimization with conserved length protein region targeting, and also incorporates domains, coding sequence position, U6 termination (TTT), restriction sites, polymorphisms and specificity. Finally, we demonstrate superior performance of the PINCER library compared to alternative genome-wide CRISPR libraries in head-to-head validation. PINCER is available for individual gene knockout and genome-wide screening for both the human and mouse genomes.

Epigenetic reprogramming by tumor-derived EZH2 gain-of-function mutations promotes aggressive 3D cell morphologies and enhances melanoma tumor growth

In addition to genetic alterations, cancer cells are characterized by myriad epigenetic changes. EZH2 is a histone methyltransferase that is over-expressed and mutated in cancer. The EZH2 gain-of-function (GOF) mutations first identified in lymphomas have recently been reported in melanoma (~2%) but remain uncharacterized. We expressed multiple EZH2 GOF mutations in the A375 metastatic skin melanoma cell line and observed both increased H3K27me3 and dramatic changes in 3D culture morphology. In these cells, prominent morphological changes were accompanied by a decrease in cell contractility and an increase in collective cell migration. At the molecular level, we observed significant alteration of the axonal guidance pathway, a pathway intricately involved in the regulation of cell shape and motility. Furthermore, the aggressive 3D morphology of EZH2 GOF-expressing melanoma cells (both endogenous and ectopic) was attenuated by EZH2 catalytic inhibition. Finally, A375 cells expressing exogenous EZH2 GOF mutants formed larger tumors than control cells in mouse xenograft studies. This study not only demonstrates the first functional characterization of EZH2 GOF mutants in non-hematopoietic cells, but also provides a rationale for EZH2 catalytic inhibition in melanoma.

Abstract 1968: Breast cancer cells escape from chemotherapy and hypoxia by distinct mechanisms

Cancer relapse following treatment remains a significant barrier to achieving cures for many patients. An emerging framework for addressing this problem focuses on cancer stem cells (CSCs). Clinical and preclinical data suggest that CSCs survive chemotherapy and antiangiogenic therapy. In breast cancer, CSCs are marked by the cell surface expression of CD44, the major receptor for hyaluronic acid. The SKBR3 cell line was previously shown to be a clinically relevant model of breast CSCs in vivo, and we have further developed this model to enable mechanistic studies of tumor relapse in vitro. We found that chemotherapy and hypoxia both enriched for CD44hi populations in SKBR3, but surprisingly, the populations were phenotypically distinct. CD44hi cells from chemotherapy but not hypoxia exhibited increased tumor cell growth and increased sensitivity to the CSC-specific inhibitor salinomycin, compared to CD44lo cells. To examine these CD44hi and CD44lo populations further, we performed transcriptional profiling with sorted cells. We found that the growth factor TGF beta-2 was upregulated in chemotherapy-treated CD44hi cells and also enhanced the growth of these cells, which suggests that TGF beta-2 autocrine/paracrine signaling can promote the growth of surviving cells. We also observed an increase in xCT (SLC7A11) expression upon chemotherapy treatment and identified the CD44v8-10 variant expressed in the CD44hi SKBR3. CD44v could therefore stabilize xCT and promote survival by lowering intracellular reactive oxygen species (ROS). We have also established a functional role for CD44 in SKBR3 cell growth: CD44 knockdown prevented colony formation, and conversely the CD44 ligand hyaluronic acid enhanced colony formation. These findings indicate that CD44 not only marks CSC populations that arise in response to chemotherapy but also functions in their survival. Our work suggests that mechanisms of tumor relapse vary based on the particular therapy, and defining these mechanisms will allow for the development of novel therapeutic strategies to enable long-term responses in the clinic.

Citation Format: Siobhan O'Brien, Liang Chen, Wenyan Zhong, Douglas Armellino, Maximillian Follettie, Marc Damelin. Breast cancer cells escape from chemotherapy and hypoxia by distinct mechanisms. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1968. doi:10.1158/1538-7445.AM2014-1968

Abstract 3487: CA9 expression highly correlates with cancer stem cell markers during passaging of PDX lines

Tumor-Initiating Cells (TICs), or Cancer Stem Cells (CSCs), are considered a subpopulation of cells within a tumor that are particularly aggressive because when isolated, these cells can form secondary tumors. Along these lines, experiments in which fragments of tumors, derived from primary patient samples, are re-implanted into nude mice, the majority of cells within the fragment die. However, day 3 after re-implantation, a small subpopulation emerges that is able to seed a new tumor. We hypothesized that these cells are unique and rare within the original tumor and consequently present an opportunity to identify novel markers that can identify these aggressive tumor cells. After sorting live human cells from tumor fragments three days after passaging, we used single cell PCR to determine the extent of heterogeneity within the fragment population. We, in fact, found that there is a subpopulation that highly expresses markers of proliferation and stemness. This is in contrast to the major population within the fragment that is enriched for genes associated with hypoxia and stress response. Interestingly, we found that the hypoxia responsive gene, CA9, does not correlate with other markers of hypoxia, such as VEGF, when analyzing cells derived from the fragment. Instead, CA9 was highly expressed among cells that were also enriched for markers such as Ki67, survivin, and Lgr5. To confirm if CA9 does identify a more proliferative, stem-like population, we have sorted CA9+ and CA9- cells from three day PDX fragments and analyzed using DNA microarrays and real-time PCR. We have consistently found, among several different PDX lines, that passaging of tumors followed by sorting CA9+ cells enriches for cells with increased levels of Lgr5, ASCL2, CD133, and Ki67. This is also validated through IHC analysis in which the majority of the cells that are positive for Ki67 are also positive for CA9. We are continuing to investigate the tumorigenicity of these cells by reinjecting CA9+ and CA9- cells from fragments back into immune-compromised mice. Furthermore, we are building a gene list derived from the microarrays to inspect by single cell PCR if any of these genes associate with Lgr5 in a grown tumor. Thus, we believe this is a functionally relevant and novel method for identify novel TIC markers.

Citation Format: Julia Friedman, Wenyan Zhong, Christine Loreth, Veronica Diesl, Xin Han, Justin Lucas, Andrea Hooper, Vlad Buklan, Edward Rosfjord, Danielle Leahy, Judy Lucas, Maximillian Follettie, Kim Arndt. CA9 expression highly correlates with cancer stem cell markers during passaging of PDX lines. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3487. doi:10.1158/1538-7445.AM2014-3487

Abstract 3138: Development of a tetracycline-inducible lentiviral system for RNAi screen in PDX tumors

Patient-derived xenograft (PDX) tumors are believed to be more clinically relevant pre-clinical models for cancer target identification and validation. We used a tetracycline-inducible lentiviral vector that delivers shRNA expression which is tightly linked to a GFP reporter in PDX cells. Using shRNAs against PLK1 (polo-like kinase 1) as positive controls, we demonstrated that three of the four PLK1 hairpins resulted in growth inhibition of HT29 and A549 cells upon dox induction. Correspondingly, these 3 hairpins showed significant knockdown of PLK1 mRNA. To facilitate RNAi in PDX tumors, we have established an in vitro system to culture PDX tumor cells. Gene expression and IHC study demonstrated that tumors regenerated from colon PDX cells grown in vitro retained features of their parental tumors. PDX cells cultured in vitro also remained tumorigenic. When GFP/shRNA-transduced colon PDX cells were re-implanted in mice to form tumors, approximately 30% of the new tumor cells was GFP-positive, enabling us to capture shRNA-expressing cells by flow cytometry. Initial shRNA drop-out screens were carried out in HT29 and colon PDX cells transduced with a pool of ∼600 shRNAs targeting a set of potential cancer associated genes. Included amongst the hairpins demonstrating statistically significant depletion in HT29 were the exact same three PLK1 shRNAs previously functionally validated. These results demonstrated that we have established a robust in vivo shRNA drop-out screening platform in PDX tumors for identification of novel cancer drug targets.

Citation Format: Lei Chen, Yi Geng, Dave Fruhling, Wenyan Zhong, Veronica Diesl, Jing Pan, Christine Loreth, Elizabeth Wang, Yaroslava Bulynko, Kim Arndt, Maximillian Follettie. Development of a tetracycline-inducible lentiviral system for RNAi screen in PDX tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3138. doi:10.1158/1538-7445.AM2013-3138

Cerberus-like is a secreted factor with neutralizing activity expressed in the anterior primitive endoderm of the mouse gastrula

We report the isolation of mouse cerberus-like (cer-l), a gene encoding a novel secreted protein that is specifically expressed in the anterior visceral endoderm during early gastrulation. Expression in the primitive endoderm starts before the appearance of the primitive streak and lasts until the head-fold stage. In later stages, a second region of expression is found in newly formed somites. Mouse cer-l shares some sequence similarity with Xenopus cerberus (Xcer). In Xenopus assays cer-l, like Xcer, mRNA acts as a potent neuralizing factor that induces forebrain markers and endoderm, but is unable to induce ectopic head-like structures as Xcer does. In addition to cer-l, anterior visceral endoderm was found to express the transcription factors Lim1, goosecoid and HNF-3beta that are also present in trunk organizer cells. A model of how head and trunk development might be regulated is discussed. Given its neuralizing activity, the secreted protein Cer-l is a candidate for mediating inductive activities of anterior visceral endoderm.