CTD² Supported Reagents
Overview
To accelerate the cancer target discovery, the Cancer Target Discovery and Development (CTD²) Network aims to disseminate knowledge, data, tools, and resources with the scientific community. This page provides a list of materials (including plasmids, cell lines, cell models) that are generated by CTD²-supported research and are available for use by researchers.
Each reagent listed is accompanied by a short description; more detailed information can be obtained from the generating laboratory (contact information provided). Some reagents are available through a distributor, while others are available directly from the generating laboratory. Many of these reagents require material transfer agreements (MTAs) for use. The requestor should work directly with the generating institution to complete the MTA. The Center for Cancer Genomics will not be responsible for obtaining the MTA but will provide information for contacting the generating laboratory.
Candidate Cancer Allele cDNA Collection
CTD² researchers at the Broad Institute/DFCI have developed a collection of plasmids including mutant alleles found in sequencing studies of cancer. It includes somatic variants found in lung adenocarcinoma and across other cancer types. The clones enable researchers to characterize the function of the cancer variants in a high throughput experiments. These plasmids are collectively called the “Broad Target Accelerator Plasmid Collections”. The design and construction of these plasmids is described in the manuscripts listed below and are available through a distributor: https://www.addgene.org/kits/boehm-target-accelerator-cancer-collection/.
References
Primary
- Kim E, et al. Systematic functional interrogation of rare cancer variants identifies oncogenic alleles. Cancer Discovery. 2016 Jul;6(7):714-26. (PMID: 27147599)
- Berger AH, Brooks AN, Wu X, et al. High-throughput phenotyping of lung cancer somatic mutations. Cancer Cell. 2016 Aug 8;30(2):214-28. (PMID: 27478040)
Supporting
- Rohban M, et al. Systematic morphological profiling of human gene and allele function via Cell Painting. Elife. 2017 Mar 18;6. pii: e24060. (PMID: 28315521)
- Johannessen C, et al. Progress towards precision functional genomics in cancer. Current Opinion in Systems Biology. (2):73-82. Download here)
- Yang X, et al. A public genome-scale lentiviral expression library of human ORFs. Nature Methods. 2011 Jun 26;8(8):659-61. (PMID: 21706014)
cDNA Clones with Rare and Recurrent Mutations Found in Cancers
The CTD² Center at UT-MD Anderson Cancer Center has developed a High-Throughput Mutagenesis and Molecular Barcoding (HiTMMoB)1,2 pipeline to construct mutant alleles open reading frame expression clones that are either recurrent or rare in cancers. These barcoded genes can be used for context-specific functional validation, detection of novel biomarkers (pathway activation) and targets (drug sensitivity). The list of available gene expression clones can be accessed here: MDACC ORF Clones.xlsx
Contact: Gordon B. Mills
References
1. Dogruluk T, et al. Identification of variant-specific functions of PIK3CA by rapid phenotyping of rare mutations. Cancer Research. 2015 Dec 15;75(24):5341-54. (PMID: 26627007)
2. Tsang YH, et al. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nature Communications. 2016 Jan 25;7:10500. (PMID: 26806015)
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Plasmids
CTD² researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes. The CRISPR/dCas9 system has several advantages: i) enables robust gene repression (CRISPRi) or activation (CRISPRa) in human cells, ii) allows specific knockdown with minimal off-target effects in human cells, iii) works efficiently in human and yeast cells, and iv) does not cause double-strand breaks. Plasmid design and construction for CRISPRi (human and yeast cells) are described in the manuscript listed below and are available through a distributor. https://www.addgene.org/crispr/qi-weissman/
Reference
Gilbert LA, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18;154(2):442-51. (PMID: 23849981)
Protein–Protein Interactions Reagents
A large number of gene mutations give proteins new capabilities to bind cellular proteins and create new signaling pathways that drive tumor growth. To discover and validate mutation-created protein-protein interactions (PPI) as therapeutic targets for cancer, the CTD² Center at Emory University has created PPI expression vector libraries. A list of available cancer-associated genes can be accessed here: Emory_CTD²_PPI_Reagents.xlsx
Contact: Haian Fu
Reference
Li Z, et al. The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. Nature Communications. 2017 Feb 16;8:14356. (PMID: 28205554)