Adam Bass - US grants

[unreadable] DESCRIPTION (provided by applicant): As a physician trained in medical oncology, I aim to develop the skills necessary to allow me to become an independent translational physician-scientist. The goal of this proposal is to identity the genetic basis for carcinomas of the stomach and esophagus with the eventual hope to develop improved treatments for these disorders based on genetic insights into disease pathogenesis. The sponsor of this application, Matthew Meyerson, has developed techniques to study genomic aberrations in cancer using high-density SNP arrays and other novel sequencing and genotyping technologies. As a basis for genomic discovery and characterization we have built a collection of DNA samples derived from fresh-frozen gastric and esophageal carcinomas and will have access to >100 gastrointestinal carcinoma cell lines. Using these arrays, our early data shows frequent recurrent genomic aberrations in gastric and esophageal carcinomas. Many of these aberrations target tyrosine kinases, suggesting that subgroups of patients with these diseases may benefit from treatments with targeted inhibition of these kinases. We have also identified a novel amplification in squamous aerodigestive carcinomas and have initiated functional studies to validate this new potential oncogene. [unreadable] [unreadable] The Specific Aims are: [unreadable] 1. To generate and analyze high-density SNP array data from over 300 carcinomas and cell lines of the stomach and esophagus to identify regions of amplification and deletion. [unreadable] 2. To genotype a panel of over 300 gastric and esophageal carcinoma primary samples and cell lines for over 1000 annotated mutations in 83 cancer-associated genes and build a collection of genomically annotated cell lines for use in validation studies. [unreadable] 3. To validate a new putative oncogene in squamous aerodigestive carcinomas and subsequently validate other candidate genes in selected copy-number alterations in gastric and esophageal carcinomas. [unreadable] [unreadable] Relevance: This project will use genomic tools to identify critical genetic alterations in a large panel of gastric and esophageal cancer samples and will use more traditional laboratory techniques to follow-up candidate genes identified through genomic studies. Through this work, we have the potential to identify and validate critical drug targets in these diseases. Results of these studies could directly lead to development of improved therapeutic strategies for patients with these deadly malignancies. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Esophageal squamous cell carcinoma (SCC) is a common and deadly disease that kills >400,000 people worldwide each year. A major barrier to improved outcomes is the lack of mechanistically-based (i.e., targeted) therapies. Through studying the role of the transcription factor oncogene SOX2 in esophageal SCC, we propose to advance our mechanistic understanding of this disease and identify new potential therapeutic vulnerabilities. We will follow upon our recent discovery that developmental transcription factor SOX2 is an oncogene subject to amplification or overexpression in the majority of esophageal SCCs. SOX2 is not only selectively subject to genomic amplification in SCCs but it is also essential for the normal development and proliferation of the esophageal squamous epithelium, suggesting a connection between the squamous cell carcinogenesis and transcriptional programs that maintain the squamous esophageal lineage. More recently, we found a novel physical and function interaction of SOX2 with the squamous transcription factor p63, specifically the oncogenic ?Np63 isoform. Our discovery of this SOX2/p63 complex in SCC, we hypothesize, reveals a master transcriptional regulatory complex controlling survival and proliferative programs in the squamous lineage, programs frequently hijacked by SCCs. Additionally, our results suggest a new mechanism by which SOX2/p63 promotes SCC. We found that SOX2 and p63 jointly regulate factors promoting oncogenic signaling including ETV4, AP-1 transcription factors FOS and JUN and their activator, HRAS. Our results further suggest another mechanistic hypothesis for SOX2 activity in cancer, that AP-1 factors further interact with SOX2 to regulate gene expression in SCC. Our proposed focused inquiry into the activity of SOX2/p63 and SOX2/AP-1 provides an opportunity to identify squamous-specific SOX2 functions and mechanisms of SCC, leading to the identification of new candidate vulnerabilities in these tumors In Aim 1, we propose test our hypothesis that p63 is essential for the oncogenic function and activity of SOX2 in esophageal SCC carcinogenesis in vivo and in cultured cells. We will test the effects of loss of p63 upon SOX2 functions in both in vitro and in vivo models. Furthermore, we will jointly analyze experimental data on SOX2/p63 activity in SCC model systems with data on primary patient data from The Cancer Genome Atlas and systematically interrogate lead candidate SOX2 targets to identify novel dependencies in these cancers. In Aim 2 we propose to test our mechanistic hypotheses by charactering the interaction of SOX2 with AP-1 factors and delineating the joint functions of SOX2 with AP-1 factors in SCC. Overall, this research contributes to public health by greatly expanding our understanding on the mechanisms of an oncogene recurrently amplified a set of common and deadly cancers that have sparse effective therapies. This work is designed to specifically enhance understanding of the driving mechanisms of these cancers thus allowing us to ultimately develop more effective targeted therapies.

? DESCRIPTION (provided by applicant): Squamous cell carcinomas of the lung and head and neck are common and highly lethal cancers for which there are no approved targeted therapies associated with a genetic biomarker. Our previous studies have nominated Fibroblast Growth Factor Receptors (FGFRs) as candidate therapeutic targets in these diseases, though clinical activity of FGFR inhibitors has been modest to date despite a few cases of dramatic response. This goal of this proposal is to develop optimized strategies for the use of FGFR inhibitors in squamous cell carcinomas, in which amplification, mutation and translocation of FGFR genes are common. The long-term objective is to enable the successful clinical application of FGFR-targeted therapies in squamous cell cancers given the urgent need to introduce effective therapies for these diseases. This proposal is unique in that it leverages extensive and novel resources at the Dana-Farber Cancer Institute/Harvard Cancer Center and incorporates the study of cancer cell lines, transgenic mouse models, patient-derived xenografts, novel FGFR antagonists and patient specimens from ongoing clinical trials of FGFR inhibitors. The proposed Specific Aims are to: 1) Evaluate known and novel recurrent FGFR alterations for oncogenicity and FGFR inhibitor sensitivity using cell line and mouse models, 2) Develop strategies to overcome acquired resistance to FGFR kinase inhibition, and 3) Define the genomic context of FGFR kinase alterations and co-dependencies in cancer cell lines and patient specimens and evaluate strategies to target co-dependencies. These studies will define which somatic FGFR alterations identified in patients with squamous cell carcinomas are the most likely to be therapeutic targets through the development and characterization of cellular model systems, transgenic animals and patient-derived xenografts. For FGFR alterations validated to confer sensitivity to FGFR inhibitors we will use cellular and murine models and tumor specimens from subjects on clinical trials of FGFR inhibitors to identify mechanisms of acquired resistance and develop strategies to overcome resistance. In cases in which oncogenic FGFR alterations do not confer sensitivity to FGFR inhibition we will identify the genomic events accounting for primary resistance and utilize cellular and animal model systems to define approaches to overcome resistance by targeting co-dependencies. Through these Aims we intend to define the optimal ways in which to apply FGFR inhibitors clinically with the ultimate goal of improving outcomes for patients with squamous cell carcinomas.

DESCRIPTION (provided by applicant): This application represents the competitive renewal of a Specialized Program of Research Excellence (SPORE) in Gastrointestinal Cancer originating from the Gastrointestinal (GI) Malignancies Program of the Dana-Farber/Harvard Cancer Center (DF/HCC). The main goal of the DF/HCC SPORE in GI Cancer is the translation of biological and technological advances into improvements in prevention, diagnostics, predictors of outcome, and advances in the treatment of gastrointestinal malignancies. The DF/HCC SPORE in GI Cancer includes researchers from all Harvard-affiliated hospitals and institutions: the Dana-Farber Cancer Institute, the Brigham and Women's Hospital, the Massachusetts General Hospital, the Beth Israel Deaconess Medical Center, Children's Hospital of Boston, Harvard Medical School, Harvard School of Public Health, and Broad Institute. Five major projects are proposed including: 1) Molecular imaging for detection of high grade dysplasia in Barrett's Esophagus; 2) Defining the role of vitamin D in colorectal carcinogenesis and cancer survival; 3) Identifying novel therapeutic strategies for KRAS-mutant colorectal cancer; 4) Overcoming resistance to RAF inhibition in BRAF-mutant colorectal cancer; and 5) Overcoming Resistance to KIT/PDGFRA Inhibition in GIST. These projects will be integrated by three cores: 1) Administration, Evaluation & Planning; 2) Tissue & Pathology; and 3) Biostatistics & Bioinformatics. The SPORE application outlines a Developmental Projects Program that includes a plan of selection of new projects and documents 18 highly innovative and productive developmental projects that have been supported during the current funding cycle. We also include a Career Development Program that outlines a mechanism for the identification and support of talented young investigators in GI cancer and report on our success in supporting and mentoring 15 young investigators during the current funding cycle. The projects and cores proposed in this application are highly integrated with present DF/HCC core resources, and involve key collaborations with investigators from other existing SPOREs and cancer centers. The renewal of this GI SPORE at DF/HCC will combine leading Harvard researchers in basic, translational, and clinical sciences into a program that has the focus and coordination required to produce meaningful advances in the diagnosis, treatment, and prevention of GI cancers.

PROJECT SUMMARY This project focuses upon Diffuse Gastric Cancer (DGC), a frequently lethal cancer, marked by its characteristic growth patterns with lack of cellular cohesion, highly invasive spread and marked propensity for metastasis. This proposal builds upon new progress in the study of DGC, bringing together a collaborative team of investigators with provocative new findings regarding the role of RHOA in the pathogenesis of this disease and several newly developed mouse model systems. These data and resources bring new opportunities to substantively advance the study of these deadly and understudied cancers. A first set of data underlying this application followed our recent identification of a novel stem cell population in gastric glands marked by Mist1 expression (Yokoyama et al, Cancer Cell 2015). These cells were demonstrated to give rise to DGC following engineered loss of tumor suppressor Cdh1. However, development of DGC required the secretion of Wnt5a by cells in the stem cell niche, with Wnt5a acting by activating GTPase RhoA in the Cdh1- null gastric cells. In parallel, we made a set of novel genomic discoveries, finding that ~20- 30% of DGCs harbor genomic aberrations impacting RHOA, either highly recurrent missense mutations of RHOA or a recurrent fusion gene including ARHGAP26, a RHOA regulator (TCGA, Nature, 2014). In this context, delineating the functions of RhoA in DGC pathogenesis, spanning both the role of Wild-type RHOA following Cdh1 loss and the oncogenic functions of RHOA mutations, emerge as critical paths towards the identification of therapeutic targets and understanding of basic pathophysiology of DGC formation. In our first Aim, we evaluate activation of wild-type RHOA in normal gastric corpus stem cells, and in early progression of Cdh1- deficient diffuse gastric cancer. We propose to test our hypothesis that RHOA is a mediator of Wnt5a effects upon corpus stem cells, especially following Cdh1 loss. These results will have immediate relevance to the definition of mechanisms of DGC initiation, clearly informing efforts to prevent and treat these deadly cancers. Our second aim evaluates RHOA somatic mutations in the initiation and progression of diffuse gastric cancer. In this aim we further characterize the biochemical and phenotypic effects of highly recurrent missense mutations of the RHOA GTPase identified in DGC. We will also functionally validate which RHOA effectors are essential for oncogenic activity of these mutants in both in vitro and in vivo systems, including our novel DGC mouse model driven by Cdh1 loss and RhoA mutation. Through these studies we hope to determine mechanisms of RHOA mediated transformation and identify specific pathways that are critical to the pathogenesis of DGC, findings with immediate potential relevance to the development of new therapeutic targets.

Project Summary The intent of this SPORE award is to create a flexible research program that responds rapidly to new advances in basic science by implementing changes in patient care. This challenge can only be undertaken if its governing body has the ability and authority to continuously monitor research plans and progress and make changes when necessary to ensure that research conducted by the SPORE maintains its translational focus. In addition, this program must be able to draw upon the resources of a large research infrastructure in order to achieve its ambitious goals. The purpose of the Administration, Evaluation and Planning Core is to coordinate the varied components of the DF/HCC GI SPORE necessary to provide oversight and leadership of the scientific, administrative and fiscal aspects of the SPORE. The Administration Core's specific aims are: Aim 1: Select projects, monitor research progress, and plan for the future Aim 2: Foster collaborative research within the SPORE and between SPOREs Aim 3: Integrate the GI Cancer SPORE into the structure of the DF/HCC Aim 4: Provide necessary resources and fiscal oversight Aim 5: Promote rapid dissemination of significant research findings and facilitate resource exchange between the DF/HCC SPORE and other institutions

Project Summary This is a competitive renewal application for a SPORE in Gastrointestinal (GI) Cancers originating from the GI Malignancies Program of the Dana-Farber/Harvard Cancer Center (DF/HCC). Since its inception in 2007, the SPORE has established a thriving culture of inter-institutional collaboration that has united basic, clinical, and population scientists into a highly productive translational enterprise. The ability to attract and retain researchers from diverse disciplines has fostered fundamental discoveries in cancer biology, innovative translational hypotheses, and cutting-edge clinical trials. The SPORE has also maintained a central focus on developing a large cadre of new investigators, building on a successful model of interdisciplinary, cross- campus cooperation that serves as a nidus for inter-SPORE relationships and other collaborations. Moreover, the SPORE has created invaluable research resources, such as the Tissue, PDX and Organoid Repository and clinical, pathology, and genomics databases that collectively accelerate translational investigation. Each of the current projects has achieved or exceeded its translational goals, providing a foundation for programmatic studies, including independent large-scale collaborative initiatives. Building on this progress, the DF/HCC GI SPORE seeks to continue to translate biological and technological advances into improvements in the prevention and treatment of GI malignancies. The overarching objectives of a renewed SPORE are to: 1) Define optimal genomic and functional strategies, including integration of cell-free (cf)DNA profiling (Projects 1-4), to predict drug responsiveness and improve diagnostics, prognostics, and clinical decisions. 2) Elucidate the interplay between oncogenic mutations, targeted therapy, and anti-tumor immunity to inform cancer biology and improve the outcome of patients with GI cancers (Projects 1,3, 4). 3) Define mechanisms of resistance to novel targeted therapies and hence identify new approaches to overcome resistance and better select the patients most likely to respond to therapy (Projects 1-4). 4) Enhance study of deadly GI cancers that, despite rising incidence, remain under- studied (Project 2, 4). 5) Encourage collaboration and promote academic rigor by providing clinical specimens, fostering core technologies and resources, and hosting regular research meetings and seminars focused on GI cancers. 6) Provide mentorship and training for young GI cancer researchers and recruit leading translational investigators from other fields through Career Enhancement and Developmental Project Awards.

Project Summary ERBB2 is amplified in ~20% of Gastric and esophageal adenocarcinomas (GEAs) and metastatic ERBB2+ GEAs are treated with a combination of chemotherapy and the antibody Trastuzumab. However, Trastuzumab is only modestly effective in GEA, and all other targeted agents in ERBB2+ breast cancer have failed in GEA clinical trials. We propose to directly address the two primary factors that we hypothesize to mediate failure of ERBB2 therapy in GEA: adaptive resistance and genetic complexity. To perform these studies, our team of investigators with complementary skill sets will both perform detailed assessment of optimal approaches to stably inhibit ERBB2 using an array of patient-derived model systems. Furthermore, we will perform a prospective clinical collection spanning multiple large academic medical centers in which we evaluate the genetic evolution of ERBB2+ GEAs during therapy, define genetic alterations that accompany resistance and then functionally validate mechanisms of resistance and optimal combination therapy. We will also explore the role of cell-free (cf)DNA genomic profiling to guide therapy in the face of genomic evolution of the disease during therapy. The overall goal will be to validate candidate resistance mechanisms and seek to define optimal combination therapies that can overcome them. We therefore propose the following Specific Aims: Aim 1: To define mechanisms of adaptive resistance to ERBB2 therapy in GEA patient samples and to develop optimal targeted combinations to stably inhibit ERBB2 activity in GEA model systems. Aim 2: To evaluate genetic etiologies of resistance by determining how frequently resistance results from ERBB2-negative subclones or from secondary genomic alterations in ERBB2+ tumor cells. Aim 3: To validate mechanistically the capacity of secondary genomic alterations to promote Trastuzumab resistance and to test combination therapies to overcome resistance. In summary, we will define genetic and non- genetic mechanisms of resistance to ERBB2 therapy. Ideally, our studies will lead to the development of active/optimal candidate therapies that work well in first-line therapy as well as in in tumors marked by acquired resistance to current therapy.

Gastrointestinal Malignancies Program Project Summary / Abstract The overarching goals of the Program are to prevent, detect early, and manage more accurately and effectively the treatment of GI malignancies. The Program will take full advantage of cutting-edge genomic technologies to identify genetic and epigenetic changes that are important in initiation and progression of GI cancers, as well as their response to therapy. Given the complexity and heterogeneity of GI malignancies, the Program had historically emphasized pancreatic and colorectal cancers, two of the four leading causes of US cancer deaths. However, with the expanding expertise and accomplishments of the Program in the other GI cancers during the previous funding period, the Program has intensified efforts in hepatobiliary, esophagogastric, and neuroendocrine tumors. The program has 95 members, representing seven DF/HCC institutions and 12 academic departments. In 2014 peer-reviewed grant funding attributed to the Program was $5.9 million in total costs from the NCI and $5.3 million from other sponsors. During the current funding period, Gastrointestinal Malignancies Program members published 2,003 cancer-relevant papers. Of these 33% were inter-institutional, 24% were intra-programmatic, and 45% were inter-programmatic collaborations between two or more DF/HCC members. Overall, when counted once, 27% of DF/HCC publications were inter- programmatic collaborations.