Advances in understanding the cancer genome have led to the development of novel therapeutics that
target distinct alterations in protein products of cancer DNA. The resulting targeted therapies, together with
protein-targeting immunotherapies, have led to significant advances in cancer patient survival. However, not all
patients benefit from these new therapies and instead many cancers continue to be treated with DNA double-
strand break (DSB)-generating radio- and chemo- therapies.
Nucleic acid targeting approaches such as the CRISPR-Cas9 system now enable investigation of a new
modality for experimental cancer therapeutics: targeting DNA directly rather than its protein products. This
proposal is aimed at the initial investigation and evaluation of this modality.
Hypothesis: Targeted induction of DNA DSBs at multiple rearrangement junctions, specific to the cancer
genome, can lead to cancer-cell specific cytotoxicity and spare damage to healthy tissue.
Specific Aim 1. Characterize the landscape of cancer-specific Cas9-targetable genomic sites across
cancers and cancer cell lines. In this aim, a computational pipeline will be developed to characterize the spectrum
of Cas9-targetable genome alterations across the Cancer Cell Line Encyclopedia and Pan-Cancer Analysis of
Whole Genomes databases of over 300 cancer cell lines and 2500 cancer genomes. Sequence features that
may affect target effectiveness in cancer therapy will be characterized, including target clonality, target copy
number, and the distribution of targetable genomic alterations across cancer types. This pipeline will become a
publicly available tool to generate lists of Cas9-targetable rearrangement breakpoints for use in future studies.
Aim 2. Develop methods to induce cytotoxicity in cancer cells using Cas9 targeted to cancer-specific
DNA rearrangement breakpoints. In a series of proof-of-principle experiments, this aim will assess whether Cas9
can induce targeted cell death through targeting DNA breaks to either single highly amplified sites or several
unique sites in the cancer neo-genome and whether this generates toxicity in healthy tissue.
Aim 3. Identify protein factors responsible for resistance or sensitivity to Cas9-mediated DNA damage:
This aim will comprise a CRISPR knockout screen to discover proteins that affect cell sensitivity to multiple Cas9-
induced DNA breaks.
This proposal will provide training in cancer genomics and targeted therapeutics under the guidance of
Professor Matthew Meyerson at Dana-Farber Cancer Institute, who is experienced in both fields. In addition to
experimental and computational research, the applicant will present results at conferences, train future scientists,
and interact with colleagues and mentors in the cancer genomics, genome editing, and cancer therapeutics
fields. The planned research is intended to culminate in publication in peer-reviewed journals. Ultimately, this
training should prepare the applicant for a career as research faculty at a United States research institution.