Memorial Sloan Kettering Cancer Center
Principal Investigators
Simon Powell, M.D., Ph.D.
Chair, Department of Radiology Oncology
Memorial Sloan Kettering Cancer Center
Sloan Kettering Institute for Cancer Research
1275 York Avenue
New York, NY 10065-6007
212-639-3639
Sarat Chandarlapaty, M.D., Ph.D.
Naddisy Foundation Chair in Breast Cancer Research
Memorial Sloan Kettering Cancer Center
Sloan Kettering Institute for Cancer Research
1275 York Avenue
New York, NY 10065-6007
212-639-3639
Overview
The research projects proposed in this Specialized Program of Research Excellence (SPORE) address genomic instability in breast cancer. The two main areas of study focus are: homologous recombination deficiency and chromosomal instability. In addition, we are continuing to study how APOBEC gene mutagenesis can influence breast cancer adaptation, including developing resistance to treatment. 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 of breast cancer development and progression. There are opportunities for therapeutic advances in breast cancer. These opportunities 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 (CIN), which does not necessarily have a unique pattern of mutations, is associated with a poor prognosis. However, there is no specific therapeutic strategy at present. The link has been established between chromosomal instability and innate immune signaling. The current goal is to exploit this connection for therapy. We have shown that chronic CIN can lead to suppression of innate immune signaling. We plan to reactivate the signaling in favor of anti-tumor response.
Project 1: Defining and Targeting Homologous Recombination Deficiency in Breast Cancer
Project Co-Leaders
- Simon Powell, M.D., Ph.D. (Clinical Co-Leader)
- Agnel Sfeir, Ph.D. (Basic Co-Leader)
Specific Aims
Genome instability, often driven by mutations in DNA repair genes, is a hallmark of breast cancer. Homologous recombination deficiency is prevalent in breast cancer up to a level of approximately 25%. Large-scale structural variant alterations to the genome have been observed in these tumors. If double-strand junctions are sequenced in detail, it is possible to categorize these tumors with more specific defects in the DNA repair pathway. The defect in DNA repair creates a vulnerability that has been exploited for cancer treatment through synthetic lethality, exemplified by PARP inhibitors (PARPi) used in homologous recombination deficient (HRD) tumors, such as those with BRCA1 or BRCA2 mutations. While effective, resistance to PARPi is now a significant clinical challenge, often driven by BRCA reversion mutations.
DNA polymerase theta (Polθ), a key player in the alternative end-joining (alt-EJ) DNA repair pathway, has emerged as a critical factor in promoting tumor survival in HRD cells and potentially driving PARPi resistance. Polθ-mediated repair is particularly associated with microhomology-mediated end joining (MMEJ), a mutagenic pathway that leaves characteristic scars across the genome and detected at reversion mutations in BRCA1 and BRCA2.
In the first aim, we investigate the distinct roles of Polθ's helicase and polymerase domains in single strand annealing, another survival pathway for HRD cells. Both domains broaden the mechanisms of how Polθ inhibitors work in preventing the survival of HRD cells. In the second aim, we explore the role of Polq in breast cancer resistance to PARPi and the development of BRCA reversion mutations. By applying advanced methods, including a fluorescent reporter assay and CRISPR/Cas9-enabled sequence-based assays, we aim to elucidate the molecular mechanisms underlying Polθ's role in the acquisition of reversion mutations. Furthermore, we will leverage in vivo models to test the therapeutic potential of Polθ inhibitors in combination with PARPi. In Aim 3, we focus on the development of PARPi resistance in patients and the implementation of a Polθ helicase domain inhibitor clinical trial from a phase I study and ultimately to a phase II efficacy study.
This work has the potential to improve long-term outcomes for patients with BRCA-mutant and other HRD cancers by overcoming major hurdles in current cancer treatment: greater cell killing and preventing resistance to PARPi.
Project 2: Targeting Innate Immune Pathways in Breast Cancers with Chromosomal Instability
Project Co-Leaders
- Adam Schmitt, M.D. (Clinical Co-Leader)
- Andy Minn M.D., Ph.D. (Basic Co-Leader)
Specific Aims
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.
CIN is a hallmark of aggressive breast cancers (and other cancer types), correlating with immune evasion, metastasis, and therapeutic resistance. Yet, why CIN promotes aggressive properties is poorly understood. CIN generates aberrant DNA (e.g., micronuclei) to activate innate immune signaling through cGAS/STING, which is typically associated with anti-tumor immunity. Indeed, acute activation of cGAS/STING increases interferon (IFN) and IFN-stimulated genes (ISGs), important immune stimulatory effectors. For example, ISGs such as OAS and RNASEL enhance the immunostimulatory effects of RNA packaged in extracellular vesicles secreted by cancer cells, leading to immune infiltration and response to immune checkpoint blockade.
However, chronic inflammation and persistent innate immune signaling can, in contrast, cause immune suppression. Consistent with this, persistently engaged cGAS-STING engenders pro-tumor properties and dampens IFN signaling (tachyphylaxis). Similarly, chronic IFN signaling in cancer cells can result in pro-tumor and immunosuppressive properties due to acquisition of “inflammatory memory”. Chronic IFN signaling in cancer cells leads to epigenetic reprogramming and altered IFN signaling through transcription factors STAT1 and IRF3 to favor expression of a subset of ISGs called “memory ISGs”. Memory ISGs are enriched in immune evasion genes, contributing to the ability of cancer cells to promote immune suppression. Thus, multiple mechanisms enable cancer cells to adapt to chronic activation of IFN, resulting in pro-tumor and immunosuppressive properties that may contribute to why CIN promotes aggressive behavior of breast and other cancers. Interfering with these adaptive mechanisms driven by CIN may unlock therapies that can otherwise activate immunogenic IFN signaling, including radiation and STING agonists.
In the first project period, we assessed the status of cGAS-STING in CIN-high human triple negative Breast Cancer (BrCa). We made the unexpected observation that levels of cancer cell-intrinsic STING protein are inversely proportional to the frequency of micronuclei with cGAS staining. This inverse relationship derives from a negative feedback loop whereby chronic CIN-dependent cGAS activation promotes STING degradation and compromises activation of IFN, suggesting inhibiting CIN and/or persistent cGAS activation may restore immunogenic IFN signaling. In separate work, we discovered that immunosuppression through chronic IFN and inflammatory memory in cancer cells can be antagonized with inhibitors of JAK and TBK1 to block STAT1 and IRF3, respectively. Thus, we hypothesize in CIN BrCa that chronic cGAS and IFN signaling leads to resistance to STING-activating therapies through tachyphylaxis and/or inflammatory memory and resistance can be reversed with inhibitors of cGAS and/or JAK and TBK1. These hypotheses will be tested in pre-clinical experiments and biomarker developments leading to novel clinical trials incorporating cGAS inhibitors and STING agonists.
Administrative Core
Core Co-Directors
Specific Aims
The Administrative Core serves as the operational hub of the SPORE. The Core will be responsible for arranging all SPORE related functions in scientific review, intra- and inter-SPORE collaborations, financial management of budgeting and monitoring expenses, editorial services as needed and grant administration. We regard the SPORE as a forum for education and mentoring, above and beyond what is directly provided in the developmental programs, by creating an environment in which new ideas for projects can be discussed with supportive SPORE key personnel. Every year, a SPORE retreat, open to breast cancer researchers (and beyond) is held where existing projects are reviewed, alternative project options (which could be added or substituted) are considered and unsolved mysteries or provocative questions that have not received significant attention in this area of research are discussed. In concert with the retreat, coordination of the functions of the internal and external advisory boards take place. Liaison activities, in conjunction with the Memorial Sloan Kettering Cancer Center (MSKCC) breast cancer disease management team, for the identification and monitoring of the cancer patient populations required for this SPORE are performed.as well as communication with our patient advocates about our ongoing results, trials and future planning.
Biospecimens Core
Core Co-Directors
Specific Aims
The primary objectives of the Biospecimen Repository and Pathology Core are to advance and facilitate the translational research efforts of the Memorial Sloan Kettering Cancer Center (MSK) SPORE in Genomic Instability in Breast Cancer. This Core will constitute a central facility for the collection, annotation, storage, and distribution of tissue and blood biospecimens from patients enrolled in research protocols described in the SPORE. All specimens will be procured following the guidelines of the MSKCC Institutional Review Board and banked, with our direct input, by the MSK Biobank Tissue Division and Pathology Core Facility. This Core is designed to provide SPORE investigators with expert support for tissue acquisition, biospecimen selection and tissue procurement of tumor samples from both patients enrolled in the research protocols and mouse models described in this SPORE application. The Biospecimen Repository and Pathology Core performs expert histopathological evaluation, conducts specimen processing for immunophenotyping and spatial profiling, interprets immunohistochemical assays, and performs tissue microdissections and nucleic acid extractions for genomic/molecular analyses. The Core collaborates closely with the Biostatistics and Computational Analysis Core and the SPORE research teams for the interpretation of tissue-based genomic findings.
The Biospecimen Repository and Pathology Core will provide support for all translational research efforts of the Genomic Instability in Breast Cancer SPORE. The specific aims of the Core include:
(1) To maintain and expand the systematic collection, annotation, and storage of bio-specimens for translational research of breast cancers with specific patterns of DNA repair defects and/or genomic instability,
(2) To perform expert pathologic evaluation of all samples of human breast cancer and animal models of breast cancer with specific patterns of DNA repair defects and/or genomic instability along with the preparation of appropriate material for use by SPORE investigators, and
(3) To perform immunophenotypic characterization of human and animal models of breast cancers with specific patterns of DNA repair defects and/or genomic instability.
The Biospecimen Repository and Pathology Core will help mitigate the impact of common confounders in translational research studies, as well as assist in the integration and prioritization of a variety of institutional pathology systems-related development efforts. Mitigation of these common confounders will be carried out by centralizing and standardizing the pathology review, from both clinical and research settings, and by working in conjunction with other Cores within MSKCC on the processing and curation of the biospecimen materials and digital images obtained from select samples.
Biostatistics and Bioinformatics Core
Core Co-Directors
Specific Aims
The Biostatistics and Computational Genomics Core have a team of dedicated personnel with extensive experience and a strong track record of developing innovative methods. The Core will provide support in statistical and computational analysis of breast cancer sequencing data to assist the design and analysis of the SPORE research projects. The team will support and maintain sequencing pipelines and provide analytical and statistical support for the analysis of genomic instability in breast cancer. They will expand current tools to detect, quantify, and track genomic signatures of specific DNA repair defects and/or genetic instability at the tumor bulk and single cell levels, as well as probe these signatures’ effect on the microenvironment. The Core will provide centralized support for data collection, processing, quality assessment, and normalization procedures to facilitate data integration, downstream analysis and visualization; accessible to scientists with little computational background. The Core will synergize with the current infrastructure available at Memorial Sloan Kettering Cancer Center to provide the SPORE investigators not only with the state-of-the-art computational biology methods, but with novel computational tools to address specific analytical challenges germane to the success of the SPORE Research Projects.
The emerging importance of studying mutational processes at single cell resolution in the SPORE Projects requires new computational methods. This Core developed a number of new approaches for DLP+ (and other single cell whole genome sequencing (scWGS)) data including SIGNALS for allele specific copy number alteration inference, mityBayes for single cell mtDNA copy number and mutation analysis of mitochondrial genomes, PERT for analysis of copy number alterations in the context of DNA replication timing and ArtiCull for inference of point mutation processes over evolutionary time from single cell data. Long read sequencing for genomic instability in breast cancer has been valuable. We integrated long read sequencing on the PromethION platform, yielding reads of tens of kb in length, with scWGS to resolve long and complex structural variants (SVs) at the sub-clonal level. These data allow a detailed analysis of focal oncogene amplifications and the allele-specific reconstruction of tumors’ evolutionary history.
We implemented a robust analytical pipeline for scRNA analysis available to all SPORE investigators and as part of larger efforts in single cell analysis including the NIH supported Center for Integrated Cellular Analysis (Satija PI). This led to development of two new published methods for SPORE related work scRNA data. Building on CellAssign, used to identify cell types as input for ContactTracing in Project 2, we developed GeneVector which exploits mutual information to identify cell types in an unbiased setting and discovers novel transcriptional programs. The method was shown to identify altered gene expression programs in TNBC PDX treated with cisplatin. We developed TreeAlign - a method for integrating DLP+ and scRNA to uncover clone-specific gene dosage effects of (allele-specific) copy number alterations for genotype-phenotype inference of cancer cell clones. The method was exemplified in TNBC indicating transcriptional programs driven by genetic copy number alterations and those (EMT and MHC Class I) that were independent of genetic events.
Several Research Projects (RPs) and Developmental Research projects (DRPs) require methods for spatial data of varying scales. For Hematoxylin and Eosin (H&E) analysis, we implemented Orpheus- a deep learning multimodal transformer model to integrate whole slide H&E images and full text from pathology clinical reports. In this approach, we demonstrated the ability to stratify high and low risk women in the ER-positive early-stage setting. The model was fit to images from >5000 patients with a co-registered OncoTypeDx risk of recurrence score. We demonstrate at the level of AUC=0.86 that the model can identify high risk women and estimate triaging for additional testing could be performed in 30% of all cases, saving time and cost for diagnosis and treatment planning. For multiplexed tissue imaging, we developed CellGate, a deep learning pipeline for fully automated spatial immuno-phenotyping from whole-slide multiplexed tissue imaging at single cell resolution. The model was trained on over 750,000 single cell images and showed high precision-recall in reproducing expert pathology labels and validation in independent datasets. It addresses a critical need in an emerging area of AI-driven pathology, focusing on spatial immuno-phenotyping of the tumor microenvironment from whole-slide multiplexed tissue imaging data analysis. This technology can provide deep insights into the immune cell topography and differences in T cell functional states and interactions with tumor cells, empowering research in dissecting spatial tumor-immune heterogeneity with biological and clinical relevance.
In summary, this collection of novel methods, all exemplified and tested in TNBC genomes will support and implement leading edge technologies for the RPs, CEPs and DRPs of the SPORE. We will continue to improve these approaches as needed and develop project-motivated approaches to accelerate and support the PIs in RPs, Career Enhancement Programs (CEPs) and DRPs in the renewal of our program.
Developmental Research Program
Program Co-Director
Sarat Chandarlapaty, M.D., Ph.D.
Specific Aims
Breast cancers frequently harbor specific patterns of homologous recombination (HR) DNA repair defects (HRD) and/or specific patterns of genetic instability, namely chromosomal instability (CIN) and APOBEC mutagenesis. These alterations are present in a substantial proportion of breast cancers, and they are enriched in metastatic disease. Biomarkers to identify these patients reliably and to define the optimal treatments for these patients are sorely needed.
The Developmental Research Program (DRP) will play an important role in fostering translational research endeavors addressing specific patterns of DNA repair defects and/or genetic instability and their molecular basis. We will use DRP funding supplemented by institutional funds to support innovative projects by new and established investigators, which are critical to the generation of new ideas in the diagnosis and treatment of this large subset of breast cancers. Our goal is to accelerate progress towards the translational research goals of our SPORE. We will annually solicit pilot project proposals with translational potential from clinical and basic investigators within the larger MSKCC community, including Rockefeller University, New York-Presbyterian Hospital and Weill Cornell Medical College of Cornell University. We will then select the most promising new projects for support after rigorous peer review by the Leadership Committee, the Internal Advisory Board and the Patient Advocates. The opinion of external reviewers will be solicited as needed. Pilot projects will be funded for 1 year, but investigators may apply for additional funding through this same competitive process next year.
Every year the Advisory and Leadership Committee members will meet to review each research Project, Core, Career Enhancement Project and developmental pilot project. Committee members will be asked to assess whether any developmental project has progressed sufficiently and shown enough translational potential, either to add to the existing projects or to eclipse one of the full SPORE Research Projects. The Committee members will then vote and decide whether any developmental project should be advanced to full project status. If so, the budgets will be appropriately adjusted and sent for approval to the Translational Research Program (TRP) at the NCI.
Career Enhancement Program
Program Co-Director
Specific Aims
The SPORE Career Enhancement Program (CEP) aims to prepare physicians and scientists for independent careers in translational research in breast cancer. Our goal is that investigators supported through this process will spend their professional lifetimes conducting translational research in breast cancer and become academic leaders in the field. Memorial Sloan Kettering Cancer Center (MSKCC) is ideally suited for this task, because of the scientific and clinical environment at our campus and affiliated institutions, and our long tradition of training physicians and scientists of the highest caliber.
The specific aims of the Career Enhancement Program are to support the mentoring and research of junior faculty for careers in translational research in breast cancer, use a dual clinical and laboratory/population science mentorship model, and to recruit and mentor new junior faculty members to work in breast cancer translational research. Our institutional environment includes numerous NIH training grants, including a K12 grant for translational science training, a number of T32 grants to train PhDs or MDs in translational research in Oncology, a Master’s Program in Clinical Oncology (recently developed to partner with the K12 program, but open to a broader group of translational scientists in development), a Certificate Program in Clinical Investigation integrated with the Clinical and Translational Science Program at Weill Cornell, and a well-established junior faculty mentoring program.
The SPORE Career Enhancement funds will be employed to enhance the existing formal mentoring programs, while encouraging more physician trainees to focus on translational research to leverage the emerging knowledge of DNA repair defects and specific patterns of genetic instability in breast cancers to deliver targeted treatments to individual breast cancer patients. We will strive to attract basic, translational and population scientists who are interested in devoting their careers to making discoveries that have a realistic potential to translate into clinical applications.