Simon N. Powell, MD, PhD (Principal Investigator)

The research projects proposed in this SPORE address genomic instability in breast cancer. Three areas are the focus of study: homologous recombination deficiency, chromosomal instability and APOBEC mutagenesis. Our ultimate plan is to exploit tumor specific vulnerabilities by virtue of their underlying genomic instability. These different profiles of genomic instability have offered novel insights about the drivers breast cancer development and progression. There are also opportunities for therapeutic advances in breast cancer, which have emerged based on the initial successes, for example, in accurately identifying homologous recombination deficiency and by treatment with specific therapy, such as a PARP inhibitor. The plan is to optimize the use of these agents and develop novel agents for these tumors.

Chromosomal instability, which does not necessarily have a unique pattern of mutations, is associated with a poor prognosis, but no specific therapeutic strategy at present. The link between chromosomal instability and innate immune signaling has been made, and the goal is to exploit this connection for therapy. For APOBEC, we know that a characteristic pattern of SNVs is observed, but in this application, we are highlighting the role of APOBEC in the acquisition of drug resistance and introducing novel approaches for reliably identifying and therapeutically targeting breast cancers with an active APOBEC mutagenesis process. In summary, the goals are to take the risks of genomic instability (poor prognosis, rapid development of resistance) and turn genomic instability into an advantage for therapeutic targeting, thereby improving the prognosis for high-risk breast cancers.

Our SPORE includes:

  • Research Project 1. Defining and targeting homologous recombination deficiency in breast cancer
  • Research Project 2. Targeting innate immune pathways in breast cancers with chromosomal instability
  • Research Project 3. Diagnosis and treatment of APOBEC mutagenesis in Metastatic Breast Cancer 

These projects are supported by 3 shared resources and 2 programs: Administrative Core; Core A. Bioinformatics and Biostatistics Data Analysis Core; Core B. Biospecimen Repository and Pathology Core; Career Enhancement Program; and Developmental Research Program.

Research Project 1: Defining and Targeting Homologous Recombination Deficiency in Breast Cancer

Project Co-leaders:

Simon N. Powell, MD, PhD (clinical science leader)

Jorge S. Reis-Filho, MD, PhD (basic science leader)

Homologous recombination deficiency is prevalent in breast cancer up to a level of ~25%. Large-scale structural variant alterations to the genome have been observed in these tumors, but if double-strand junctions are sequenced in detail, it is possible to categorize these tumors with more specific defects in the DNA repair pathway. We assert that there are fundamentally different patterns of genome instability for the different components of double-strand break repair. One is focused on the function of the BRCA1-BRCA2 pathway, where alterations in function are frequent in breast cancers. Although traditionally perceived as equivalent, there is now evidence to demonstrate that genomic alterations that are BRCA1-like may have functional differences from those that are BRCA2-like and we are working to understand whether there are therapeutic strategies that are different for the two genotypes.

Upstream defects in DNA DSB repair are focused on sensing DNA damage (e.g. ATM or CHK2), which is another well documented mechanism for suppressing cancer formation. The DNA damage signaling defects are less well known, but are observed in many types of cancer including breast cancer. Thus, the goals of this project are to diagnose the DNA repair defect reliably and with greater resolution. Our hypothesis is that different types of DNA repair defects result in the utilization of distinct backup DNA repair mechanisms, which themselves result in specific genomic signatures and sensitivity to different therapeutic agents. Hence, we posit that upstream defects are best targeted by the use of replication checkpoint inhibitors, but that BRCA defective tumors are best treated by targeting the backup pathway, such as PARP-inhibitors or new agents beyond PARP-inhibitors.

The goal of the first aim is to apply the current genomic landscape tests of HR-deficiency and determine which method predicts most accurately the type of homologous recombination DNA repair defect (i.e. upstream DNA damage sensing, downstream BRCA1-like or downstream BRCA2-like). The ultimate goal is to devise a taxonomy based on the genomic features of DNA damage response/ homologous recombination DNA repair-deficiency, in addition to any identified target gene mutations, which will ultimately guide therapeutic options. The second aim is to generate genetically engineered cell lines to understand the developmental drivers of the genomic landscape changes. In addition, we will use these cells to test new synthetic lethal approaches to target specific subsets of breast cancers with distinct types of homologous recombination DNA repair defects. The third aim consists of human clinical trials either being conducted at Memorial Sloan Kettering or elsewhere, where we are conducting the trial or leading the analysis of the clinical bio-specimens for correlative study analyses. We will test the use of ATR-inhibitors and determine the genomic status of the tumors in responders and non-responders. Similarly, we will study the impact of the PARP-inhibitor olaparib in patients who are BRCA1/2 wild-type but harbor a germline and/or somatic genetic alteration affecting homologous recombination DNA repair-related genes. We will extend our studies to also consider the combined effects of radiotherapy in combination with either ATR-inhibitors or PARP-inhibitors.

The ultimate goal of this project is to personalize the treatment of breast cancer patients whose tumors display homologous recombination DNA repair-related defects according to their genetic and genomic features, seeking to improve substantially the outcome of these poor prognosis patients and direct the deployment of therapeutic agents already approved (e.g. olaparib) or already in clinical trials (e.g. ATR-inhibitors) or still being developed (e.g. Pol-theta or RAD52 inhibitors).

Research Project 2: Targeting Innate Immune Pathways in Breast Cancers with Chromosomal Instability

Project Co-leaders:

Samuel Bakhoum, MD (clinical science leader)

Lewis C. Cantley, PhD (basic science leader)

While considerable progress has been made in treating primary breast cancers, metastatic breast cancers remain a challenge. Metastatic breast cancer cells typically have chromosomal instability (CIN) that involves chromosome-level alterations leading to genomic copy number abnormalities. A major challenge in targeting breast cancers driven by CIN is the lack of known targetable alterations. We recently found that CIN promotes chronic inflammatory signaling in cancer cells. As chromosomes missegregate, they often become encapsulated in micronuclei. Subsequent micronuclear rupture exposes genomic double-stranded DNA to the cytosol. Cytosolic DNA activates anti-viral innate immune pathways, chief among which is cGAS-STING signaling. Under normal circumstances, cGAS-STING activation promotes type I interferon and facilitates cell-mediated immunity. Engagement of STING in normal epithelial cells induces senescence and cell death. We have shown that cancer cells, however, are intrinsically resistant to cGAS-STING activation by virtue of their chronic exposure to cytosolic DNA. Instead, they upregulate alternative pathways downstream of STING, such as NF-kB signaling.

The extent to which cancer cells depend on chronic inflammatory signaling is poorly understood. More importantly, how they subvert innate immune signaling to avoid immune surveillance remains unknown. Our ongoing work reveals that cGAS-STING signaling is sequestered in cancer cells away from the host. Furthermore, human breast tumors upregulate ENPP1, a negative regulator of cGAS-STING signaling. ENPP1 enables immune evasion by degrading cGAMP, the second messenger produced by cGAS, only in the extracellular space. As such ENPP1 prevents host STING activation in response to tumor-to-host cGAMP transfer. Strikingly, pharmacologic inhibition of STING suppresses metastasis in syngeneic models of melanoma, breast, and colon cancers. We postulate this is because its inhibition in tumor cells outweighs its protective role in the host. Building on this work, we will expand our pre-clinical testing of STING inhibition in breast cancer probing its efficacy in delaying metastasis and therapeutic resistance. We will then examine whether cGAMP contributes toward the formation of an immune suppressive microenvironment through metabolic breakdown in the extracellular space. Finally, we will develop cGAS-STING-based biomarkers in prospectively collected tumor specimens.

Research Project 3: Diagnosis and Treatment of APOBEC Mutagenesis in Metastatic Breast Cancer

Project Co-leaders:

Sarat Chandarlapaty, MD (clinical science leader)

Reuben S. Harris, PhD (basic science leader)

Although the majority of early stage estrogen receptor (ER)-positive breast cancers are cured through multimodality care, metastatic ER-positive breast cancer (MBC) remains a lethal disease. Insights into this discrepancy have come through comparative genomic analyses of primary and metastatic tumors. We and others have identified certain ‘mutational signatures’ appear to be enriched in metastatic disease. These mutational signatures represent the DNA damage and repair processes that shape the cancer genome and can give rise to the individual mutations and the transformed phenotypes they convey. Among these, the APOBEC mutational signature is both enriched and highly prevalent in ER-positive MBC, comprising the dominant mutational signature for these lethal cancers. Our preliminary data confirm that APOBEC activation can promote the development of endocrine resistance in cancer models.

In this project, we propose three aims to advance the APOBEC mutational process as a biomarker and therapeutic target in breast cancer. (1) We will develop and utilize robust bioinformatic methods to detect the presence and the timing of onset of the APOBEC mutational signature from clinical NGS datasets of both tumor and cell free DNA (cfDNA). We will further ascertain if a promising IHC assay for the A3B enzyme can identify those ER-positive cancers likely to subsequently develop an APOBEC mutational signature. (2) We will determine the mechanisms and kinetics of APOBEC’s contribution to endocrine resistance. We will use isogenic cell line models and patient derived xenografts to dissect the types of resistance patterns that are caused by APOBEC as well their timing and whether the endocrine therapy itself contributes to the induction of APOBEC activity. (3) We will assess both immunologic and synthetic lethal approaches to targeting tumors in which APOBEC activity is induced and determine their capabilities in killing APOBEC-positive cancers. We anticipate that our findings will uniquely position our team to launch clinical trials testing specific approaches to diagnose APOBEC-positive tumors, to prevent the development of resistance to endocrine therapies, and to target the largest subset of ER-positive endocrine-resistant metastatic breast cancers.