Developmental Research Program

Awarded in 2016

Award 8: Supramolecular nanotherapeutics for preferential immune modulation of the tumor microenvironment

Investigator: Ashish Kulkarni, PhD (BWH) 

  • Aim 1: Use SNPs to switch immunosuppressive M2 to cytotoxic M1 macrophages, and study the effect in breast cancer. Based on preliminary observations, we will (a) use a syngeneic immunocompetent 4T1 and an athymic MDAMB-231 TNBC xenograft murine model to test the efficacy of the SNP vs a CSFR1 antibody and small molecule inhibitors of CSF1R; and (b) dissect the mechanisms underlying the switch from a M2 to an M1 subtype in response to SNP mediated sustained CSF1R inhibition.
  • Aim 2: Test for synergy between the SNP and an immune checkpoint inhibitor in a breast cancer model. More specifically, we will test the hypothesis that a combination of a CSF1R-inhibiting SNP and an immune checkpoint inhibitor, administered in the right temporal sequence can result in an enhanced outcome in terms of survival.

Award 9: Rapid functional analysis of BRCA1 VUS alleles

Investigator: Nicholas Willis, PhD (BIDMC)

The project will test the hypothesis that Suppression of aberrant DSB repair contributes to BRCA1 tumor suppressor function.

  • Aim1: Perform a genetic analysis of a panel of BRCA1 variants in HR repair and LTGC suppression. Survey the remaining BRCA1 VUS alleles for suppression of LTGC. Generate and test efficacy of RFP-SCR breast cancer HR reporter cell lines. 
  • Aim 2: Relate HR functions of VUS alleles to PARPi sensitivity and cisplatin sensitivity. Study the impact of BRCA1 variants in reversal of PARP inhibitor sensitivity of BRCA1 mutant cells. 


Award 10: Exploiting CDK4/6 inhibitor-induced senescence in breast cancer

Investigator: Shom Goel, MBBS, PhD (DFCI)

Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) have shown great promise in the treatment of breast cancer. When breast cancer cells are treated with these agents in vitro, they undergo cell cycle arrest – an expected outcome given the mechanisms of action of these drugs. However, apoptosis has not been observed. Rather, cells undergo morphologic changes consistent the process of cellular senescence, and indeed my studies have shown that CDK4/6 inhibitor treatment actually primes breast cancer cells away from apoptosis. 

Overall Aims: In this project, I propose to study the mechanism by which CDK4/6 inhibitor treatment renders breast cancer cells resistant to apoptosis. If a molecular pathway governing this process can be found, then pharmacologic targeting of this pathway might be able to convert the cellular response to CDK4/6 inhibitors from senescence to apoptosis. Drugs that might be able to achieve this are known as “senolytics” or “senoptotics”.

Awarded in 2015

Complimenting BMN-673 with PD-1 Pathway Blockade to Improve Responses Against Brca1-/- Breast Cancer

Investigator: Michael Goldberg, PhD (DFCI)

Immunotherapy can address refractory disease and represents an exciting approach to achieve durable responses. While the antitumor effects of conventional therapies – such as radiation and chemotherapy – are generally attributed to their cyotoxicity, their efficacy is at least partly attributable to their partial induction of antitumor immunity. Still, even immunotherapy has demonstrated only modest benefit against advanced breast cancer to date. A combination of cancer cell-intrinsic and -extrinsic interventions may be required to improve outcomes. The goal of this SPORE project is to confirm that combining the PARP1 inhibitor BMN-673 with anti-PD-1 or anti-PD-L1 will yield a synergistic antitumor response against breast tumors that exhibit impaired homologous recombination, a common feature of triple-negative breast cancer.

We are the first to show that, BMN-673 has immunoregulatory effects, providing a mechanistic rationale for the proposed combination. We identified several immunoregulatory genes that are upregulated following treatment with BMN-673 and hypothesized that BMN-673 may influence the composition and function of immune cells in the tumor microenvironment. We confirmed that BMN-673 significantly increases the number of tumor-associated CD8+ T cells and NK cells as well as their production of IFN-γ and TNF-α. These data suggest that BMN-673 may therefore serve as an adjuvant therapy to immunotherapy in mice– and ultimately patients– whose tumors harbor defects in homologous recombination. To test this hypothesis, we will complete the following

  • Aim 1: confirm synergy between BMN-673 and anti-PD-1/PD-L1 in Brca1-/- breast tumors, and
  • Aim 2: define mechanism of cooperativity between PARP inhibition and PD-1 pathway checkpoint blockade.

This project is well aligned with the scope, investigators, and project selection of the SPORE in Breast Cancer. The work is highly complementary to Project 3 (Novel Strategies to Extend DNA Repair Therapies for Triple-Negative Breast Cancer). If successful, the approach described herein could be replicated with inhibitors from Project 4 (BET Bromodomain Proteins as Novel Therapeutic Targets in Triple-Negative Breast Cancer). We will work with Core D (Tissue and Pathology Core) and hope to work with Core C (Clinical Trials Core).

Neutralization of BCL2/BCL-XL enhances the cytotoxicity of T-DM1 in vivo

Investigator: Jason Zoeller, PhD (HMS)

Resistance to T-DM1 represents a major obstacle in the effective treatment. Using two PDX models of advanced HER2+ resistant disease, we obtained preliminary evidence demonstrating that blockade of BCL2/BCL-XL anti-apoptotic activity dramatically enhances the effectiveness of T-DM1. This proposal will characterize this combination treatment in additional models of advanced and/or metastatic HER2+ breast cancer, to address its effectiveness in distinct ER tumor subtypes, characterize the need for BCL2- and/or BCL-XL-specific inhibition, and assess tumor response at the primary and secondary sites. Such insight could inform a future clinical trial. Improving the initial cytotoxic effectiveness of T-DM1 may provide a therapeutic approach to reduce and/or eliminate drug resistance in the clinic.

  • Aim 1: To evaluate the effectiveness of T-DM1 plus BCL2/BCL-XL inhibition across multiple models of HER2+ resistant disease. For T-DM1/ABT-263 in vivo experiments, PDX tumor fragments or cells will be transplanted into the mammary fat pad of female NOD/SCID mice. Mice with hormone receptor positive tumors will require sub-cutaneous implantation of a slow-release estrogen pellet. The BCL2/BCL-XL inhibitor ABT-263 will be administered, and pathological response will be determined via analysis of the H&E stained sections. Tumor cells will be visualized by HER2 IHC. Tumors will also be analyzed for markers of cell proliferation (Ki67) and cell death (cleaved caspase-3).
  • Aim 2: To determine the effectiveness of combination T-DM1 plus BCL2- or BCL-XL-selective inhibitors.  We will initiate these studies in HER2+ER- PDX12 and HER2+ER+ PDX5. Experiments will include eight treatment arms: (1) T-DM1, (2) BCL2/BCL-XL inhibitor ABT-263, (3) BCL2 inhibitor ABT-199, (4) BCL-XL inhibitor ABT-133, (5) T-DM1 + ABT-263, (6) T-DM1 + ABT-199, (7) T-DM1 + ABT-133 and (8) placebo controls. ABT-133 will be provided through collaboration with Abbvie. Blood and tumors will be collected and analyzed at the 14-day endpoint as described above.

Discovering how Phosphoinositide 3-Kinase (PI3K) regulates DNA synthesis and repair, and exploiting this dual function of PI3K to design combination treatments for triple-negative breast cancer

Investigator: Gerburg Wulf, MD, PhD

  • Aim 1: Nucleoside synthesis downstream from PI3K is not regulated via AKT but via the Rac/PAK axis and ultimately regulation of glycolytic flux. PI3K directly coordinates glycolysis with cytoskeletal dynamics in an AKT-independent manner. Growth factors or insulin stimulate the PI3K-dependent activation of Rac, leading to disruption of the actin cytoskeleton, release of filamentous actin-bound aldolase A and an increase in aldolase activity. Consistently, PI3K-, but not AKT-, SGK- or mTOR-inhibitors, cause a significant decrease in glycolysis at the step catalyzed by aldolase, while activating PIK3CA mutations have the opposite effect.
  • Aim 2: DNA damage induced by PI3K inhibitors is a consequence of impaired production of nucleotides needed for DNA synthesis and DNA repair.  Inhibition of PI3K causes a reduction in all four nucleotide triphosphates, while inhibition of AKT is less effective than inhibition of PI3K in suppressing nucleotide synthesis and inducing DNA damage. Carbon flux studies reveal that PI3K-inhibition disproportionately affects the non-oxidative pentose phosphate pathway (non-ox PPP) that delivers ribose-5-posphate required for base ribosylation. In vivo in a mouse model of BRCA1-linked triple-negative breast cancer (K14-Cre BRCA1f/fp53f/f) the PI3K-inhibitor BKM120 led to a precipitous drop in DNA synthesis within 8 hours of drug treatment, while DNA synthesis in normal tissues was less affected. In this mouse model combined PI3K- and PARP-inhibition was superior to either agent alone to induce durable remissions of established tumors. 

Awarded in 2014

Developing microRNA ‘signatures’ as biomarkers for optimal therapeutic use of PARP inhibitors in Triple Negative Breast Cancer (TNBC)

Investigator: Dipanjan Chowdhury, Ph.D. (DFCI)

  • Aim 1: Assess the ability of SENSMiRNAs to abrogate HR-mediated DSB repair using two complementary assays which have been optimized in my laboratory.
  • Aim 2: Understand the mechanism by which these miRNAs influence HR, that is, identify HR pathway members that may be regulated by SENSMiRNAs.
  • Aim 3: Assess the ability of SENSMiRNAs to enhance sensitivity to PARP inhibitors alone and in combination with CDK inhibitor in vitro in TNBC lines.
  • Aim 4: Assess whether expression of SENSMiRNAs are associated with response to PARPi/CDK inhibitor (Phase II trial, SPORE program) or with cisplatin (Phase II trial, Myriad Genetic Laboratories) in tumor specimens from TNBC patients.

Identifying Disseminated Triple Negative Breast Tumor Cells that are Responsible for Disease Relapse

Investigator: Sandra S. McAllister, PhD (BWH)

  • Aim 1: Identify disseminated tumor cells that respond to systemic signals to form overt lung metastases.
  • Aim 2: Obtain molecular signatures of disseminated tumor cells before and after they form overt tumors.

Palbociclib in Breast Cancer: Resistance Mechanisms and Synthetic Lethality with NHEJ Inhibition

Investigator:  Geoffrey Shapiro, M.D., Ph.D. (DFCI)

  • Aim 1: Determine the mechanisms of resistance to the CD4/6 inhibitor palbociclib in breast cancer cell lines and investigate strategies to overcome resistance.
  • Aim 2: Assess the combined inhibition of CDK4/6 and non-homologous end joining (NHEJ) in breast cancer cells.

Elucidation of the role of MELK, a novel oncogenic kinase, in basal-like breast cancer

Investigator: Jean Zhao, PhD (DFCI)

  • Aim 1: Determine the mechanism(s) underlying the oncogenic role of MELK in basal-like breast cancer.
  • Aim 2: Evaluate the role MELK in the tumorigenesis of basal-like breast cancer in a GEM model.
  • Aim 3: Develop a GEM model of breast tumor driven by overexpression of MELK.

Developmental Research Project Publications

Choi YE, Pan Y, Park E, Konstantinopoulos P, De S, D'Andrea A, Chowdhury D. MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability. ELife. 2014 Apr 30;3:e02445.

Wang Y, Lee YM, Baitsch L, Huang A, Xiang Y, Tong H, Lako A, Von T, Choi C, Lim E, Min J, Li L, Stegmeier F, Schlegel R, Eck MJ, Gray NS, Mitchison TJ, Zhao JJ. MELK is an oncogenic kinase essential for mitotic progression in basal-like breast cancer cells. Elife. 2014 May 20;3:e01763.

Choi YE, Meghani K, Brault ME, Leclerc L, He YJ, Day TA, Elias KM, Drapkin R, Weinstock DM, Dao F, Shih KK, Matulonis U, Levine DA, Konstantinopoulos PA, Chowdhury D. Platinum and PARP Inhibitor Resistance Due to Overexpression of MicroRNA-622 in BRCA1-Mutant Ovarian Cancer. Cell Rep. 2016 Jan 26;14(3):429-39.

Hu H, Juvekar A, Lyssiotis CA, Lien EC, Albeck JG, Oh D, Varma G, Hung YP, Ullas S, Lauring J, Seth P, Lundquist MR, Tolan DR, Grant AK, Needleman DJ, Asara JM, Cantley LC, Wulf GM. Phosphoinositide 3 Kinase Regulates Glycolysis through Mobilization of Aldolase from the Actin cytoskeleton. Cell. 2016 Jan 28;164(3):433-46.

Goel S*, Wang Q, Watt AC, Tolaney SM, Dillon DA, Li W, Ramm S, Palmer AC, Yuzugullu H, Varadan V, Tuck D, Harris LN Wong K-K, Liu XS, Sicinski P, Winer EP, Krop IE, Zhao JJ*. Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Cancer Cell. 2016 Mar 14; 29(3):255-69. (*co-corresponding author) 

Juvekar A, Hu H, Yadegarynia S, Lyssiotis CA, Ullas S, Lien EC, Bellinger G, Son J, Hok RC, Seth P, Daly MB, Kim B, Scully R, Asara JM, Cantley LC, Wulf GM. Phosphoinositide 3-Kinase inhibitors induce DNA damage through nucleoside depletion. Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):e4338-47. 

Wang Y, Begley M, Li Q, Huang HT, Lako A, Eck M, Gray N, Mitchison TJ, Cantley LC, Zhao JJ. Mitotic MELK-eIF4B Signaling Controls Protein Synthesis and Tumor Cell Survival. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9810-5. Epub 2016 Aug 15.

Matulonis UA, Wulf GM, Barry WT, Birrer M, Westin SN, Farooq S, Bell-McGuinn KM, Obermayer E, Whalen C, Spagnoletti T, Luo W, Liu H, Hok RC, Aghajanian C, Solit DB, Mills GB, Taylor BS, Won H, Berger MF, Palakurthi S, Liu J, Cantley LC, Winer E. Phase I dose escalation study of the PI3kinase pathway inhibitor BKM120 and the oral poly (ADP ribose) polymerase (PARP) inhibitor olaparib for the treatment of high-grade serous ovarian and breast cancer.  Ann Oncol. 2017 Mar 1;28(3):512-518.

Zoeller JJ, Bronson RT, Selfors LM, Mills GB, Brugge JS. Niche-localized tumor cells are protected from HER2-targeted therapy via upregulation of an anti-apoptotic program in vivo. NPJ Breast Cancer. 2017 May 1;3:18.

de Oliveira Taveira M, Nabavi S, Wang Y, Tonellato P, Esteva FJ, Cantley LC, Wulf GM. Genomic characteristics of trastuzumab-resistant Her2-positive metastatic breast cancer. J Cancer Res Clin Oncol. 2017 Jul;143(7):1255-62.