An RNAi-based Functional Genetic Approach to Drug Screening and Characterization

Technology #13883

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A strategy to define combination mechanisms of drug action. (1a) An illustration of the competing hypotheses for single versus combination mechanisms. Squares denote a diagrammatic version of an shRNA signature with resistance shown in red and sensitivity in blue. A schematic of the potential results following the combinations of Drugs A and B is shown to the right. “Same mechanism” refers to the idea that a combination signature could look similar to the individual drugs used to create the combination. The different mechanism box gives examples of how combination signatures might differ from component signatures. (1 b) An outline of our signature based methodology. shRNAs targeting the 8 genes in our signature are retrovirally transduced in a mixed pool. These pools are subsequently treated with combinations of drugs and compared to a high resolution single drug signature dataset.CHOP/CVAD components work via an averaging mechanism.  A scatter plot compares bliss independence values for the pairwise combinations of cytotoxic CVAD/CHOP components to the rest of the dataset. Significance was determined using a Mann-Whitney Utest.
Professor Michael Hemann
Department of Biology, MIT
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Professor Douglas Lauffenburger
Department of Biological Engineering, MIT
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Justin Pritchard
Department of Biology, MIT
Hai Jiang
Koch Institute for Integrative Cancer Research, MIT
Managed By
Tod Woolf
MIT Technology Licensing Officer
Patent Protection

RNAi-Based Method of Screening and Characterizing Drug Combinations

US Patent Pending 2014-0206544

RNAi-Based Method of Drug Screening and Characterization

US Patent Pending 2014-0134635
A mammalian functional-genetic approach to characterizing cancer therapeutics
Nature Chemical Biology, December 26, 2010


This invention is a means of identifying the mechanism of action of cell death-inducing small molecules. It may be used by drug development companies for the identification of drug targets and mechanisms of drug resistance for a particular small molecule.

Problem Addressed

Pharmaceutical companies most commonly identify anti-cancer drugs with large screens for agents that cause cell death. Target identification of these drugs occurs later in the process and significantly hampers drug development especially when mechanism of action is never defined. Current methods to identify mechanism of action, such as microarray approaches, are expensive, lack reproducibility, and cannot efficiently differentiate between compounds that engage common downstream signaling pathways. Better understanding of mechanism of action would lead to target identification as well as insights into drug resistance. Combination chemotherapy also relies on multi-drug administration for cancer treatment with the goal of evading spontaneous resistance to single agents. Chemotherapy may be improved with greater understanding of mechanism of action for increased combinatorial efficacy of drugs.


This invention uses RNA interference (RNAi) to knockdown genes known to be involved in mediating responses to a diverse set of chemotherapeutics, with short hairpin RNAs (shRNAs). Cell-lines were then exposed to twenty common chemotherapeutics and their response monitored. The distinct set of shRNAs which promoted resistance and sensitivity for each drug were clustered to produce a functional array. Since drugs with similar mechanisms of action cluster together, the mechanism of action of small molecules may be defined. This approach has already yielded the mechanism of action of two poorly characterized drugs, apigenin and NSC3852.  Furthermore, it is highly-reproducible, simple, and flexible.


  • Simple and reproducible so that it can be performed by any laboratory with the appropriate vectors and cells
  • May be applied to a number of small molecules and combinations thereof