Ford Lab Research Focus

Senior Research Scientist/Lab Manager Lisa McPherson discussing data with PI Jim Ford

Research Focus:

The major investigative focus of our laboratory and translational research program is to explore the mammalian genetic determinants of the inducible response and cellular sensitivity to DNA damage, focusing particularly on the effects of the p53 and BRCA1 gene products on DNA repair and cancer susceptibility. We have found that loss of p53 and BRCA1 function results in defective repair of DNA damage, including effects on homologous recombination, nucleotide and base-excision repair. In addition, we are exploring ways to exploit the DNA repair deficiency of p53 and BRCA1 mutant cancer cells and to identify targeted therapeutic approaches for the treatment and prevention of related cancers.  Current research projects include:

Model for BRCA1-associated carcinogenesis. p53 mutations lead to a decrease in NER activity resulting in increased genetic instability and potentially increased tumorigenesis.

The Role of BRCA1 in Base-Excision DNA Repair (BER):

A. ODD is typically repaired by the BER pathway. Left unrepaired, ODD leads to mutagenesis, genetic instability, and ultimately tumorigenesis. BRCA1 activates BER, reduces levels of ODD, and thereby prevents tumorigenesis. When BRCA1 is mutated, DNA repair-activating agents may enhance BER of ODD, and in turn prevent tumorigenesis.

B. In the BER host cell reactivation assay, ODD is introduced into a GFP-expressing adenovirus by treatment with visible light in the presence of methylene blue.  Cells with functional BER can repair the damage and fluoresce while cells with defective BER do not. 

BRCA1 appears to have complex regulatory effects on multiple DNA repair pathways in addition to their shared role in homologous-recombination and DNA double strand break repair. We first described that breast cancer cell lines mutant for the BRCA1 gene exhibit sensitivity to oxidative DNA damage (ODD). We also developed a novel viral based “host-cell reactivation” assay to measure the repair of oxidative DNA damage in living cells using an adenoviral GFP reporter gene, and demonstrated that BRCA1 mutant cells were defective in BER. 

Discovery of small molecules that activate BER and may prevent BRCA1-associated tumors: We designed and performed a high-throughput screen to identify small-molecules that enhance DNA repair in a BRCA1 mutant background, and thus may serve as candidate agents for prevention of cancer by enhancing DNA repair and interrupting multistep mutagenesis. Several of these drugs are potentially “repurposeable” and are currently or were previously used in humans for other indications. We have shown activity of two in preventing the development of BRCA1-associated breast cancers in mice and are developing plans for a clinical trial using the lead hit for prevention of BRCA1-associated premalignant changes in ovaries from women undergoing risk-reducing bilateral oopherectomies. 

Measurement and modulation of MTH1 in cancer:

We are exploring the role of MTH1 (NUDT1) in DNA repair and cancer. MTH1 sanitizes the nucleotide pool by removing 8-oxodGTP before it is incorporated into DNA by hydrolyzing it into 8-oxodGMP. In a collaborative effort with the Kool lab in the Stanford Department of Chemistry, we have recently used a novel probe-based detection system to demonstrate increased amounts of MTH1 in colon, lung and pancreatic cancers relative to matched normal samples. We are also utilizing this probe-based assay to assess the effect of small molecules in modulating MTH1 activity in the prevention and treatment of cancer. 

The novel ARGO probe combines 8-oxodGTP and ATP to quantitatively measure MTH1 enzymatic activity in cells and tissues. The significant increast in MTH1 activity in tumors compared to matching normal tissue, indicates that MTH1 is a marker of cancer.

Clinical translation of Next-Generation Sequencing for hereditary cancer risk assessment:

Variants of uncertain significance (VUS) count, per gene, across 198 participants.

 We recently led the first clinical study of next-generation gene panel DNA sequencing among women referred for breast cancer risk assessment using germline DNA samples from our large translational research biobank containing more than 2000 specimens, all donated by individuals tested for BRCA1/2 or other gene mutations. Among 198 women meeting evidence-based guidelines for BRCA1/2 testing, we detected 16 pathogenic variants (>10%) in genes other than BRCA1/2 thus doubling the rate of identified germline cancer susceptibility gene alterations in this population, a discovery that has enabled early detection of cancers. Fifteen variants warranted discussion of more intensive screening or prevention. This is a significant yield of potentially actionable results.



Targeting TNBC and other malignancies with DNA damaging drugs and PARP:

We found through preclinical studies and clinical trials that nearly all BRCA mutation associated breast cancer, and approximately half of non-BRCA mutant TNBC exhibit clinical sensitivity to platinum chemotherapy and synthetic lethality with PARP inhibitors. As part of these efforts, we performed extensive correlative studies on tumor tissue and germline DNA samples obtained from patients enrolled in a large, multi-institutional neoadjuvant clinical trial, using gene expression microarrays, DNA copy-number analyses, and germline DNA sequencing. We described a bioinformatic measure of homologous recombination deficiency (HRD) that is highly predictive of clinical response in these patients. Our current and future research goals in this area is to leverage our expertise in germline and tumor genomics to identify patients with breast and other cancers harboring DNA repair gene defects and HRD for treatment using PARP inhibitors and other DNA repair directed therapies (ATR and DNA-PK inhibitors). We have also developed breast cancer cell lines resistant to PARP-inhibitors and are exploring the mechanism for this drug resistance.

HRD status provides significant improvement over clinical variables or BRCA1/2 mutation status in identifying tumors with an increased likelihood of response to platinum-based neoadjuvant therapy among patients with TNBC. Clinical use of the HRD test has the potential to identify sporadic TNBC patients likely to respond to DNA-damaging therapy beyond those currently identified by germline BRCA1/2 mutation screening.

James Ford, M.D.
Division of Oncology
269 Campus Dr. CCSR Rm 1115
Stanford University School of Medicine
Stanford, CA 94305-5151

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