Diehl P.,Cellecta, Inc.
Chimica Oggi/Chemistry Today
Since the fi rst human genome was sequenced over 10 years ago, a tremendous amount of data has been collected and associated with biological traits, responses, and disease processes. While this information has provided a basis for many new diagnostics, it has not stimulated signifi cant development of novel therapeutics. For new drug development, a more sophisticated understanding of how genes function is required. While there are some techniques that can be used to investigate the function of individual genes, few options exist for genome-wide functional analysis. Only two technologies currently form the basis of techniques for broad-based genetic screens that assess the functions of large numbers of genes in a single assay: RNA interference and CRISPR knockout screens. To make real progress in understanding the disease process and identifying novel therapeutic approaches, new more powerful methods are required. Source
Li H.,Karolinska Institutet |
Zhang Y.,Northeast Agricultural University |
Strose A.,Roswell Park Cancer Institute |
Tedesco D.,Cellecta, Inc. |
And 2 more authors.
Cell Death and Differentiation
The restoration of p53 tumor suppressor function is a promising therapeutic strategy to combat cancer. However, the biological outcomes of p53 activation, ranging from the promotion of growth arrest to the induction of cell death, are hard to predict, which limits the clinical application of p53-based therapies. In the present study, we performed an integrated analysis of genome-wide short hairpin RNA screen and gene expression data and uncovered a previously unrecognized role of Sp1 as a central modulator of the transcriptional response induced by p53 that leads to robust induction of apoptosis. Sp1 is indispensable for the pro-apoptotic transcriptional repression by p53, but not for the induction of pro-apoptotic genes. Furthermore, the p53-dependent pro-apoptotic transcriptional repression required the co-binding of Sp1 to p53 target genes. Our results also highlight that Sp1 shares with p53 a common regulator, MDM2, which targets Sp1 for proteasomal degradation. This uncovers a new mechanism of the tight control of apoptosis in cells. Our study advances the understanding of the molecular basis of p53-mediated apoptosis and implicates Sp1 as one of its key modulators. We found that small molecules reactivating p53 can differentially modulate Sp1, thus providing insights into how to manipulate p53 response in a controlled way. © 2014 Macmillan Publishers Limited All rights reserved. Source
Cellecta, Inc. | Date: 2014-01-13
Methods of obtaining a single cell expression profile from a target mammalian cell are provided. Aspects of the methods include contacting a cellular sample which includes the target mammalian cell with a packaged viral barcoded trans-splicing library including a plurality of barcoded trans-splicing constructs under transduction conditions, where a barcoded trans-splicing construct includes a trans-splicing element linked to a barcode element. The methods further include generating expression data from the resultant transduced target mammalian cell to obtain the single cell expression data from the target mammalian cell. Also provided are compositions, e.g., libraries and components thereof, which find use in practicing the methods.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 999.60K | Year: 2012
The DNA Damage and Repair (DDR) signaling modules are among the most commonly deregulated genes in human tumors. Deficiencies in DDR pathways are believed to influence tumorigenic processes by promoting a mutator phenotype, which contributes to the acquisition of genetic lesions and fuels malignant transformation. As DDR networks are extensively rewired in cancer cells, the concept of synthetic sickness/lethality (SL) can be exploited to identify novel therapeutic target(s) for cancer. RNA interference(RNAi) currently makes it possible to use high-throughput functional genomic strategies for SL target identification. Unfortunately, while RNAi has opened new avenues for improving the drug discovery process, these avenues remain only potential opportunities until we develop robust RNAi screening technologies, which include experimental and bioinformatics tools for drug target discovery, validation and integration into operational cell-based models. To address these issues, as outlined in the 290 SBIRcontract proposal, the development of a novel orthogonal functional genomics platform based on validated lentiviral shRNA libraries to facilitate the discovery of SL molecular targets en masse will be required. Accordingly, the ultimate goal of the 290SBIR research project is to develop and commercialize a human pooled SL shRNA library that targets all of the canonical and non-canonical DDR (400x400) gene combinations and to validate their application in RNAi screens in cancer cell models. This project will also require the development of supporting tools, including a public SL DDR database, protocols, reagents and software tools for in vitro screening, and the validation of the SL hits that specifically control the proliferation and survival of cancer cells. The aforementioned genetic screening and bioinformatic tools will provide the research community with highly modular and cost-effective approaches to understand and integrate dynamic changes in DDR signaling networks for the discovery of novelanti-cancer SL targets.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 199.68K | Year: 2010
Despite rapid advances in elucidating the molecular basis of human diseases, an ostensibly more difficult post-genomic challenge is the functional annotation of disease-specific signaling pathways and the application of this information for the development of novel drugs. RNA interference (RNAi) now makes it possible to use high-throughput functional genomic strategies for SL target identification. Unfortunately, while RNAi has opened new avenues for improving the drug discovery process, these avenues remain only potential opportunities until we develop robust RNAi screening technologies, including experimental and bioinformatics tools for data validation and integration into operational cell-based models. To address these issues and, as outlined in the 290 SBIR contract proposal, it will require to develop a novel orthogonal functional genomics platform based on validated lentiviral shRNA libraries to facilitate discovery of SL molecular targets en masse. Accordingly, the ultimate goal of the 290 topic research project is to develop and commercialize a set of human and mouse pooled SL shRNA libraries targeting all cannonical DDR gene combinations and validate their application for RNAi screens in cancer cell models. As a supporting tools, it will also require to develop protocols, reagents and software tools for in vitro and in vivo screening SL hit validation and therapeutic target prioritization that specifically control the proliferation and survival of cancer cells. The aforementioned genetic screening and bioinformatic tools will provide the research community with highly modular, cost-effective approaches to understand and integrate the dynamic changes in DDR signaling networks for the discovery of novel anti-cancer SL targets.